Edgar Filing: BROOKS AUTOMATION INC

1
AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON AUGUST 21, 2001
REGISTRATION NO. 333-____

SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

FORM S-3
REGISTRATION STATEMENT

UNDER
THE SECURITIES ACT OF 1933

BROOKS AUTOMATION, INC.
(EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

DELAWARE 04-3040660
(STATE OR OTHER JURISDICTION OF (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION) IDENTIFICATION NUMBER)

15 ELIZABETH DRIVE, CHELMSFORD, MASSACHUSETTS 01824 - (978) 262-2400
(ADDRESS, INCLUDING ZIP CODE AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

ROBERT J. THERRIEN
PRESIDENT AND CHIEF EXECUTIVE OFFICER
BROOKS AUTOMATION, INC.
15 ELIZABETH DRIVE,
CHELMSFORD, MASSACHUSETTS 01824
(978) 262-2400
(NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER,
INCLUDING AREA CODE, OF AGENT FOR SERVICE)

COPIES TO:

LAWRENCE M. LEVY, ESQUIRE
BROWN, RUDNICK, FREED & GESMER
ONE FINANCIAL CENTER
BOSTON, MA 02111
(617) 856-8200

APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC: From time
to time after the effective date of this Registration Statement.

If the only securities being registered on this form are being offered
pursuant to dividend or interest reinvestment plans, check the following box.
[ ]
If any of the securities being registered on this form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box.[x]

If this form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, check the following box and
list the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ]

If this form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

If delivery of the prospectus is expected to be made pursuant to Rule 434,
check the following box. [ ]
2

Calculation of Registration Fee

Title of Each Class of Amount of Shares to be Proposed Maximum Proposed Maximum
Securities to be Registered Registered Offering Price per Share (1) Aggregate Offering Price (1) Registration Fee
--------------------------- ---------------------- ------------------------ ------------------------ ----------------
Common Stock, par value 423,369 shares (2) $44.50 $18,839,920.50 $4,709.98
$.01
Preferred Share Purchase
Rights (3) 423,369 (3) -- -- --

(1) Estimated solely for the purpose of computing the amount of the
registration fee based on the average of the high and low prices for
the Common Stock as reported on the Nasdaq Stock Market on August 16,
2001, in accordance with Rule 457(c) under the Securities Act of 1933,
as amended.

(2) Such presently indeterminable number of additional shares of common
stock are registered hereunder as may be issued in the event of a
merger, consolidation, reorganization, recapitalization, stock
dividend, stock split, stock combination or other similar changes in
the common stock.

(3) On July 23, 1997, the Board of Directors of the Registrant declared a
dividend of one preferred share purchase right for each share of common
stock outstanding on August 21, 1997. The 423,369 rights registered by
this Registration Statement represent one right issued in connection
with each share of common stock. Such presently indeterminable number
of rights are also registered by this Registration Statement as may be
issued in the event of a merger, consolidation, reorganization,
recapitalization, stock dividend, stock split or other similar change
in common stock. The rights are not separately transferable apart from
the common stock, nor are they exercisable until the occurrence of
certain events. Accordingly, no independent value has been attributed
to the rights.

THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THIS REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE SECURITIES AND EXCHANGE COMMISSION, ACTING
PURSUANT TO SAID SECTION 8(a), MAY DETERMINE.

2
3

THE INFORMATION IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED. THE
SELLING STOCKHOLDERS MAY NOT SELL THESE SECURITIES UNTIL THE REGISTRATION
STATEMENT FILED WITH THE SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS
PROSPECTUS IS NOT AN OFFER TO SELL THESE SECURITIES AND IT IS NOT SOLICITING AN
OFFER TO BUY THESE SECURITIES IN ANY STATE WHERE THE OFFER OR SALE IS
PROHIBITED.

Subject to Completion,
Dated August 21, 2001

BROOKS AUTOMATION, INC.

COMMON STOCK

423,369 SHARES

The selling stockholders are selling all of the shares of common stock
offered by this prospectus. We will not receive any of the proceeds from the
sale of these shares.

The selling stockholders may offer the common stock through public or
private transactions, at prevailing market prices, or at privately negotiated
prices.

Our common stock is quoted on the Nasdaq National Market under the
symbol "BRKS". On August 20, 2001, the last reported sale price of the common
stock on the Nasdaq National Market was $43.51 per share.

INVESTING IN THE SECURITIES OFFERED HEREBY INVOLVES A HIGH DEGREE OF
RISK. SEE "RISK FACTORS" BEGINNING ON PAGE 2.

THE SECURITIES AND EXCHANGE COMMISSION AND STATE SECURITIES REGULATORS
HAVE NOT APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

This prospectus is dated _________, 2001.
4

TABLE OF CONTENTS

PROSPECTUS SUMMARY ................................................ 1

RISK FACTORS ...................................................... 2

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS ................. 11

USE OF PROCEEDS ................................................... 12

SELLING STOCKHOLDERS .............................................. 12

PLAN OF DISTRIBUTION .............................................. 14

LEGAL MATTERS ..................................................... 15

EXPERTS ........................................................... 15

WHERE YOU CAN FIND MORE INFORMATION ............................... 15

YOU SHOULD RELY ONLY ON THE INFORMATION CONTAINED IN THIS DOCUMENT OR TO
WHICH WE HAVE REFERRED YOU. WE HAVE NOT AUTHORIZED ANYONE TO PROVIDE YOU WITH
INFORMATION THAT IS DIFFERENT. THIS DOCUMENT MAY BE USED ONLY WHERE IT IS LEGAL
TO SELL THESE SECURITIES. THE INFORMATION IN THIS DOCUMENT MAY ONLY BE ACCURATE
ON THE DATE OF THIS DOCUMENT.

i
5

PROSPECTUS SUMMARY

This summary provides an overview of selected information and may not
contain all of the information that is important to you. You should read the
entire prospectus carefully, including the financial data, related notes and the
information we have incorporated by reference before making an investment
decision.

ABOUT BROOKS

We are a leading supplier of integrated tool and factory automation
solutions for the global semiconductor manufacturing and related industries. We
have distinguished ourselves as a technology and market leader, particularly in
the demanding cluster-tool vacuum-processing environment and in integrated
factory automation software applications. Our automation solutions are designed
to optimize equipment and factory productivity. These solutions include tool
automation modules, complete semiconductor wafer handling systems, factory
interface solutions and automation software and integration services.

We are a Delaware corporation. Our principal offices are located at 15
Elizabeth Drive, Chelmsford, Massachusetts 01824 and our telephone number is
(978) 262-2400. Our corporate website is www.brooks.com. The information on our
website is not incorporated by reference in this prospectus.

THE OFFERING

The selling stockholders may offer and sell up to 423,369 shares of our
common stock under this prospectus. The first selling stockholder, KLA-Tencor
Technologies Corporation, a wholly-owned subsidiary of KLA-Tencor Corporation,
obtained shares offered by this prospectus in connection with our acquisition of
the e-diagnostics infrastructure assets of KLA-Tencor Corporation and the
selling stockholder on June 26, 2001. The second selling stockholder, Ben Mahy,
obtained shares offered by this prospectus in connection with our acquisition of
SimCon, N.V. on May 15, 2001 The other selling stockholders, the former
stockholders of CCS Technology, Inc., obtained shares offered by this prospectus
in connection with our acquisition of CCS Technology, Inc. on June 25, 2001.
6

RISK FACTORS

This offering involves a high degree of risk. You should carefully consider
the risks described below and the other information in this prospectus before
deciding to invest in shares of our common stock. While these are the risks and
uncertainties we believe are most important for you to consider, you should know
that they are not the only risks or uncertainties facing us or which may
adversely affect our business. If any of the following risks or uncertainties
actually occurs, our business, financial condition and operating results would
likely suffer. In that event, the market price of our common stock could decline
and you could lose all or part of the money you paid to buy our common stock.

This prospectus also contains forward-looking statements that involve risks
and uncertainties. Our actual results could differ materially from those
anticipated in these forward-looking statements as a result of certain factors,
including the risks faced by us described below and elsewhere in this
prospectus.

RISK FACTORS RELATING TO OUR OPERATIONS

THE CYCLICAL DEMAND OF SEMICONDUCTOR MANUFACTURERS AFFECTS OUR OPERATING
RESULTS.

Our business is significantly dependent on capital expenditures by
semiconductor manufacturers. The level of semiconductor manufacturers' capital
expenditures is dependent on the current and anticipated market demand for
semiconductors. The semiconductor industry is cyclical and is currently
experiencing a downturn. We anticipate we will have lower shipments of our
products during the next few quarters. Despite this expected reduced volume, we
plan to continue to invest in those areas which we believe are important to our
long-term growth, such as our infrastructure, customer support and new product
development. As a result, consistent with our experience with downturns in the
past, we believe the existing industry downturn will lead to reduced revenues
for us and may cause us to incur losses.

OUR SALES VOLUME DEPENDS ON THE SALES VOLUME OF OUR ORIGINAL EQUIPMENT
MANUFACTURER CUSTOMERS AND ON INVESTMENT IN MAJOR CAPITAL EXPANSION PROGRAMS BY
SEMICONDUCTOR MANUFACTURING COMPANIES.

We sell a majority of our tool automation products to original equipment
manufacturers that incorporate our products into their equipment. Therefore, our
revenues are directly dependent on the ability of these customers to develop,
market and sell their equipment in a timely, cost-effective manner. We also
generate significant revenue in from large orders by semiconductor manufacturing
companies that build new plants or invest in major automation retrofits. Our
revenue is dependent, in part, on continued capital investment of semiconductor
manufacturing companies.

WE RELY ON A SMALL NUMBER OF CUSTOMERS FOR A LARGE PORTION OF OUR REVENUES.

We receive a significant portion of our revenues in each fiscal period from
a limited number of customers. The loss of one or more of these major customers,
or a decrease in orders by one or more customers, would adversely affect our
business. Sales to our ten largest customers accounted for approximately 42% of
total revenues in the nine months ended June 30, 2001 and 43% of total revenues
in fiscal 2000. Sales to Lam Research Corporation, our largest customer,
accounted for approximately 9% of our total revenues for the nine months ended
June 30, 2001 and for the fiscal year ended September 30, 2000.

DELAYS IN OR CANCELLATION OF SHIPMENT OF A FEW OF OUR LARGE ORDERS COULD
SUBSTANTIALLY DECREASE OUR REVENUES.

Historically, a substantial portion of our quarterly and annual revenues has
come from sales of a small number of large orders. These orders consist of
products with high selling prices compared to our other products. As a result,
the timing of when we recognize revenue from one of these large orders can have
a significant impact on our total revenues and operating results for a
particular period. Our operating results could be harmed if a small number

2
7
of large orders are canceled or rescheduled by customers or cannot be filled due
to delays in manufacturing, testing, shipping or product acceptance.

WE HAVE SIGNIFICANT FIXED COSTS WHICH ARE NOT EASILY REDUCED IF REVENUES FALL
BELOW EXPECTATIONS.

Our expense levels are based in part on our future revenue expectations.
Many of our expenses, particularly those relating to capital equipment and
manufacturing overhead, are relatively fixed. If we do not meet our sales goals
we may be unable to rapidly reduce these fixed costs. Our ability to reduce
expenses is further constrained because we must continue to invest in research
and development to maintain our competitive position and to maintain service and
support for our existing global customer base. Accordingly, if we suffer an
unexpected downturn in revenue, our inability to reduce fixed costs rapidly
could increase the adverse impact on our operations.

OUR LENGTHY SALES CYCLE REQUIRES US TO INCUR SIGNIFICANT EXPENSES WITH NO
ASSURANCE THAT WE WILL GENERATE REVENUE.

Our tool automation products are generally incorporated into original
equipment manufacturer equipment at the design stage. To obtain new business
from our original equipment manufacturer customers, we must develop products for
selection by a potential customer at the design stage. This often requires us to
make significant expenditures, without any assurance of success. The original
equipment manufacturer's design decisions often precede the generation of volume
sales, if any, by a year or more. We also must complete successfully a lengthy
evaluation and proposal process before we can achieve volume sales of our
factory automation software to our factory automation customers. We cannot
guarantee that we will continue to achieve design wins or satisfy evaluations by
our end-user customers of our software. We cannot guarantee that the equipment
manufactured by our original equipment manufacturing customers will be
commercially successful. If we or our original equipment manufacturing customers
fail to develop and introduce new products successfully and in a timely manner,
our business and financial results will suffer.

OUR INTERNATIONAL BUSINESS OPERATIONS EXPOSE US TO A NUMBER OF DIFFICULTIES IN
COORDINATING OUR ACTIVITIES ABROAD AND IN DEALING WITH MULTIPLE REGULATORY
ENVIRONMENTS.

Approximately 48% of our total revenues in the nine months ended June 30,
2001, and 49% of our total revenues in fiscal 2000, were derived from customers
located outside North America. We anticipate that international sales will
continue to account for a significant portion of our revenues. Our vendors are
located in several different foreign countries. As a result of our international
business operations, we are subject to various risks, including:

- difficulties in staffing and managing operations in multiple
locations in many countries;

- challenges presented by collecting trade accounts receivable
in foreign jurisdictions;

- possible adverse tax consequences;

- governmental currency controls;

- changes in various regulatory requirements;

- political and economic changes and disruptions; and

- export/import controls and tariff regulations.

To support our international customers, we maintain locations in several
countries, including Canada, Germany, Japan, Malaysia, Singapore, South Korea,
Taiwan and the United Kingdom. We cannot guarantee that we will be able to
manage these operations effectively. We cannot assure you that our investment in
these international operations will enable us to compete successfully in
international markets or to meet the service and support needs
3
8
of our customers, some of whom are located in countries where we have no
infrastructure.

Although our international sales are primarily denominated in U.S. dollars,
changes in currency exchange rates can make it more difficult for us to compete
with foreign manufacturers on price. If our international sales increase
relative to our total revenues, these factors could have a more pronounced
effect on our operating results.

WE MUST CONTINUALLY IMPROVE OUR TECHNOLOGY TO REMAIN COMPETITIVE.

Technology changes rapidly in the semiconductor, data storage and flat panel
display manufacturing industries. We believe our success depends in part upon
our ability to enhance our existing products and to develop and market new
products to meet customer needs. We cannot guarantee that we will identify and
adjust to changing market conditions or succeed in introducing commercially
rewarding products or product enhancements. The success of our product
development and introduction depends on a number of factors, including:

- accurately identifying and defining new market opportunities and products;

- completing and introducing new product designs in a timely manner;

- market acceptance of our products and our customers' products;

- development of a comprehensive, integrated product strategy; and

- efficient implementation and installation services.

WE FACE SIGNIFICANT COMPETITION WHICH COULD RESULT IN DECREASED DEMAND FOR OUR
PRODUCTS OR SERVICES.

The markets for our products are intensely competitive and we may be unable
to compete successfully. We believe that our primary competition in the tool
automation market is from integrated original equipment manufacturers that
satisfy their semiconductor and flat panel display handling needs internally
rather than by purchasing systems or modules from an independent supplier like
us. Many of these original equipment manufacturers have substantially greater
resources than we do. Applied Materials, Inc., the leading process equipment
original equipment manufacturer, develops and manufactures its own central wafer
handling systems and modules. We may not be successful in selling our products
to original equipment manufacturers that internally satisfy their wafer or
substrate handling needs, regardless of the performance or the price of our
products. Moreover, integrated original equipment manufacturers may begin to
commercialize their handling capabilities and become our competitors.

We believe that the primary competitive factors in the end-user
semiconductor manufacturer market for factory automation software and process
control software are product functionality, price/performance, ease of use, ease
of integration, hardware and software platform compatibility, vendor reputation
and financial stability. The relative importance of these competitive factors
may change over time. We directly compete in this market with various
competitors, including Applied Materials-Consilium, PRI, IBM and numerous small,
independent software companies. We also compete with the in-house software
staffs of semiconductor manufacturers like NEC. Most of those manufacturers have
substantially greater resources than we do.

We believe that the primary competitive factors in the factory interface
market are technical and technological capabilities, reliability,
price/performance, ease of integration and global sales and support capability.
In this market, we compete directly with Asyst, Fortrend, Kensington and Rorze.
Some of these competitors have substantial financial resources and extensive
engineering, manufacturing and marketing capabilities.

MUCH OF OUR SUCCESS AND VALUE LIES IN OUR OWNERSHIP AND USE OF INTELLECTUAL
PROPERTY AND OUR FAILURE TO PROTECT THAT PROPERTY COULD ADVERSELY AFFECT OUR
FUTURE GROWTH.

Our ability to compete is heavily affected by our ability to protect our
intellectual property. We rely primarily

4
9
on trade secret laws, confidentiality procedures, patents, copyrights,
trademarks and licensing arrangements to protect our intellectual property. The
steps we have taken to protect our technology may be inadequate. Existing trade
secret, trademark and copyright laws offer only limited protection. Our patents
could be invalidated or circumvented. The laws of certain foreign countries in
which our products are or may be developed, manufactured or sold may not fully
protect our products or intellectual property rights. This may make the
possibility of piracy of our technology and products more likely. We cannot
guarantee that the steps we have taken to protect our intellectual property will
be adequate to prevent misappropriation of our technology. There has been
substantial litigation regarding patent and other intellectual property rights
in semiconductor-related industries. We may engage in litigation to:

- enforce our patents;

- protect our trade secrets or know-how;

- defend ourselves against claims alleging we infringe the rights of
others; or

- determine the scope and validity of the patents or intellectual
property rights of others.

Any litigation could result in substantial cost to us and divert the attention
of our management, which could harm our operating results and our ability to
grow.

OUR OPERATIONS COULD INFRINGE ON THE INTELLECTUAL PROPERTY RIGHTS OF OTHERS.

Particular aspects of our technology could be found to infringe on the
intellectual property rights or patents of others. Other companies may hold or
obtain patents on inventions or may otherwise claim proprietary rights to
technology necessary to our business. We cannot predict the extent to which we
may be required to seek licenses or alter our products so that they no longer
infringe the rights of others. We cannot guarantee that the terms of any
licenses we may be required to seek will be reasonable. Similarly, changing our
products or processes to avoid infringing the rights of others may be costly or
impractical or could detract from the value of our products.

OUR BUSINESS MAY BE HARMED BY INFRINGEMENT CLAIMS OF GENERAL SIGNAL OR APPLIED
MATERIALS.

We received notice from General Signal Corporation alleging certain of our
products infringed its patent rights. The notification advised us that General
Signal was attempting to enforce its rights to those patents in litigation
against Applied Materials, and that, at the conclusion of that litigation,
General Signal intended to enforce its rights against us and others. According
to a press release issued by Applied Materials in November 1997, Applied
Materials settled its litigation with General Signal by acquiring ownership of
five General Signal patents. Although not verified by us, these five patents
would appear to be the patents referred to by General Signal in its prior notice
to us. Applied Materials has not contacted us regarding these patents.

WE DO NOT HAVE LONG-TERM CONTRACTS WITH OUR CUSTOMERS AND OUR CUSTOMERS MAY
CEASE PURCHASING OUR PRODUCTS AT ANY TIME.

We generally do not have long-term contracts with our customers. As a
result, our agreements with our customers do not provide any assurance of future
sales. Accordingly:

- our customers can cease purchasing our products at any time without
penalty;

- our customers are free to purchase products from our competitors;

- we are exposed to competitive price pressure on each order; and

- our customers are not required to make minimum purchases.

5
10

OUR OPERATING RESULTS WOULD BE HARMED IF ONE OF OUR KEY SUPPLIERS FAILS TO
DELIVER COMPONENTS FOR OUR PRODUCTS.

We currently obtain many of our components on an as needed, purchase order
basis. We do not have any long-term supply contracts with our vendors. When
demand for semiconductor manufacturing equipment increases, our suppliers face
significant challenges in providing components on a timely basis. Our inability
to obtain components in required quantities or of acceptable quality could
result in significant delays or reductions in product shipments. This would
materially and adversely affect our operating results.

RISING ENERGY COSTS IN CALIFORNIA MAY RESULT IN INCREASED OPERATING EXPENSES AND
REDUCED NET INCOME.

California is currently experiencing an energy crisis. As a result, energy
costs in California, including natural gas and electricity, may rise
significantly over the next several months relative to the rest of the United
States. Because we maintain one of our manufacturing facilities in Southern
California, our operating expenses with respect to that facility may increase if
this trend continues. If we cannot pass along these costs to our customers, our
margins will suffer and our net income could decrease.

OUR FUTURE GROWTH COULD BE HARMED IF THE COMMERCIAL ADOPTION OF 300MM WAFER
TECHNOLOGY CONTINUES TO PROGRESS SLOWLY OR IS NOT ADOPTED BY THE INDUSTRY.

Our future growth relies in part on the adoption of new systems and
technologies to automate the processing of 300mm wafers. However, the industry
transition from the current, widely used 200mm manufacturing technology to 300mm
manufacturing technology is occurring more slowly than expected. A significant
delay in the adoption of 300mm manufacturing technology, or the failure of the
industry to adopt 300mm manufacturing technology, could significantly reduce our
opportunities for future growth. Moreover, continued delay in transition to
300mm technology could permit our competitors to introduce competing or superior
300mm products at more competitive prices. As a result of these factors,
competition for 300mm orders could become vigorous and could harm our results of
operations.

OUR RECENT RAPID GROWTH IS STRAINING OUR OPERATIONS AND REQUIRING US TO INCUR
COSTS TO UPGRADE OUR INFRASTRUCTURE.

During the last calendar year, we have experienced extremely rapid growth in
our operations, the number of our employees, our product offerings and the
geographic area of our operations. Our growth has placed a significant strain on
our management, operations and financial systems. Our future operating results
will be dependent in part on our ability to continue to implement and improve
our operating and financial controls and management information systems. If we
fail to manage our growth effectively, our financial condition, results of
operations and business could be harmed.

WE MAY BE UNABLE TO RECRUIT AND RETAIN NECESSARY PERSONNEL BECAUSE OF INTENSE
COMPETITION FOR HIGHLY SKILLED PERSONNEL.

We need to retain a substantial number of employees with technical
backgrounds for both our hardware and software engineering and support staffs.
The market for these employees is intensely competitive, and we have
occasionally experienced delays in hiring these personnel. Due to the cyclical
nature of the demand for our products and the current downturn in the
semiconductor market, we recently reduced our workforce by approximately 4% as a
cost reduction measure. If the semiconductor market experiences an upturn, we
may need to rebuild our workforce. Due to the competitive nature of the labor
markets in which we operate, this type of employment cycle increases our risk of
not being able to retain and recruit key personnel. Our inability to recruit,
retain and train adequate numbers of qualified personnel on a timely basis could
adversely affect our ability to develop, manufacture, install and support our
products.

6
11
OUR SYSTEMS INTEGRATION SERVICES BUSINESS HAS GROWN SIGNIFICANTLY RECENTLY AND
OUR POOR EXECUTION OF THOSE SERVICES COULD ADVERSELY IMPACT OUR OPERATING
RESULTS.

The number of projects we are pursuing for our systems integration services
business has grown significantly recently. This business consists of integrating
combinations of our software and hardware products to provide more comprehensive
solutions for our end-user customers. The delivery of these services typically
is complex, requiring that we coordinate personnel with varying technical
backgrounds in performing substantial amounts of services in accordance with
timetables. We are in the early stages of developing this business and we are
subject to the risks attendant to entering a business in which we have limited
direct experience. In addition, our ability to supply these services and
increase our revenues is limited by our ability to retain, hire and train
systems integration personnel. We believe that there is significant competition
for these personnel with the advanced skills and technical knowledge that we
need. Some of our competitors may have greater resources to hire personnel with
that skill and knowledge. Our operating margins could be adversely impacted if
we do not effectively hire and train additional personnel or deliver systems
integration services to our customers on a satisfactory and timely basis
consistent with our budgets.

CHANGES TO ACCOUNTING STANDARDS AND RULES COULD ADVERSELY AFFECT THE TIMING OF
WHEN WE RECOGNIZE REVENUE.

In December 1999, the Securities and Exchange Commission issued Staff
Accounting Bulletin No. 101, or SAB 101, "Revenue Recognition in Financial
Statements". SAB 101 provides guidance on applying generally accepted accounting
principles to revenue recognition issues in financial statements. While we have
not fully assessed the impact on us of the adoption of SAB 101, it may require a
portion of our quarterly revenues to be deferred. Any change in our revenue
recognition policy resulting from the implementation of SAB 101 would be
reported as a change in accounting principle in the quarter in which we
implemented SAB 101, with a cumulative adjustment in that quarter to reflect the
effect of the change. As a result, while SAB 101 would not affect the
fundamental aspects of our operations as measured by our shipments and cash
flows, implementation of SAB 101 could have an adverse affect on our reported
results of operations in the quarter that SAB 101 is implemented.

RISK FACTORS RELATING TO OUR ACQUISITIONS

OUR BUSINESS COULD BE HARMED IF WE FAIL TO ADEQUATELY INTEGRATE THE OPERATIONS
OF OUR ACQUISITIONS.

Our management must devote substantial time and resources to the integration
of the operations of our acquired businesses with our core business and with
each other. If we fail to accomplish this integration efficiently, we may not
realize the anticipated benefits of our acquisitions. The process of integrating
supply and distribution channels, research and development initiatives, computer
and accounting systems and other aspects of the operation of our acquired
businesses, presents a significant challenge to our management. This is
compounded by the challenge of simultaneously managing a larger entity. We have
completed a number of acquisitions in a short period of time. These businesses
have operations and personnel located in Asia, Europe and the United States and
present a number of additional difficulties of integration, including:

- assimilating products and designs into integrated solutions;

- informing customers, suppliers and distributors of the effects of the
acquisitions and integrating them into our overall operations;

- integrating personnel with disparate business backgrounds and cultures;

- defining and executing a comprehensive product strategy;

- managing geographically remote units;

7
12

- managing the risks of entering markets or types of businesses in which
we have limited or no direct experience; and

- minimizing the loss of key employees of the acquired businesses.

If we delay the integration or fail to integrate an acquired business or
experience other unforeseen difficulties, the integration process may require a
disproportionate amount of our management's attention and financial and other
resources. Our failure to adequately address these difficulties could harm our
business and financial results.

OUR BUSINESS MAY BE HARMED BY ACQUISITIONS WE COMPLETE IN THE FUTURE.

We plan to continue to pursue additional acquisitions of related businesses.
Our identification of suitable acquisition candidates involves risks inherent in
assessing the values, strengths, weaknesses, risks and profitability of
acquisition candidates, including the effects of the possible acquisition on our
business, diversion of our management's attention and risks associated with
unanticipated problems or latent liabilities. If we are successful in pursuing
future acquisitions, we will be required to expend significant funds, incur
additional debt or issue additional securities, which may negatively affect our
results of operations and be dilutive to our stockholders. If we spend
significant funds or incur additional debt, our ability to obtain financing for
working capital or other purposes could decline and we may be more vulnerable to
economic downturns and competitive pressures. We cannot guarantee that we will
be able to finance additional acquisitions or that we will realize any
anticipated benefits from acquisitions that we complete. Should we successfully
acquire another business, the process of integrating acquired operations into
our existing operations may result in unforeseen operating difficulties and may
require significant financial resources that would otherwise be available for
the ongoing development or expansion of our existing business.

RISK FACTORS RELATING TO OUR COMMON STOCK

OUR OPERATING RESULTS FLUCTUATE SIGNIFICANTLY, WHICH COULD NEGATIVELY IMPACT OUR
BUSINESS AND OUR STOCK PRICE.

Our margins, revenues and other operating results can fluctuate
significantly from quarter to quarter depending upon a variety of factors,
including:

- the level of demand for semiconductors in general;

- cycles in the market for semiconductor manufacturing equipment and
automation software;

- the timing and size of orders from our customer base;

- our ability to manufacture, test and deliver products in a timely and
cost-effective manner;

- our success in winning competitions for orders;

- the timing of our new product announcements and releases and those of our
competitors;

- the mix of products we sell;

- competitive pricing pressures; and

- the level of automation required in fab extensions, upgrades and new
facilities.

We entered the factory automation software business in fiscal 1999. We
believe a substantial portion of our revenues from this business will be
dependent on achieving project milestones. As a result, our revenue from this

8
13
business will be subject to fluctuations depending upon a number of factors,
including whether we can achieve project milestones on a timely basis, if at
all, as well as the timing and size of projects.

OUR STOCK PRICE IS VOLATILE.

The market price of our common stock has fluctuated widely. For example,
between April 4, 2001 and April 30, 2001, the closing price of our common stock
rose from approximately $35.45 to $62.61 per share and between July 17, 2000 and
August 10, 2000, the price of our common stock dropped from approximately $68.00
to $35.38 per share. Consequently, the current market price of our common stock
may not be indicative of future market prices, and we may be unable to sustain
or increase the value of an investment in our common stock. Factors affecting
our stock price may include:

- variations in operating results from quarter to quarter;

- changes in earnings estimates by analysts or our failure to meet analysts'
expectations;

- changes in the market price per share of our public company customers;

- market conditions in the industry;

- general economic conditions;

- low trading volume of our common stock; and

- the number of firms making a market in our common stock.

In addition, the stock market has recently experienced extreme price and
volume fluctuations. These fluctuations have particularly affected the market
prices of the securities of high technology companies like us. These market
fluctuations could adversely affect the market price of our common stock.

BECAUSE A LIMITED NUMBER OF STOCKHOLDERS, INCLUDING A MEMBER OF OUR MANAGEMENT
TEAM, OWN A SUBSTANTIAL NUMBER OF OUR SHARES AND ARE PARTIES TO VOTING
AGREEMENTS, DECISIONS MADE BY THEM MAY BE DETRIMENTAL TO YOUR INTERESTS.

By virtue of their stock ownership and voting agreements, Robert J.
Therrien, our president and chief executive officer, Jenoptik AG and Daifuku
America Corporation have the power to significantly influence our affairs and
are able to influence the outcome of matters required to be submitted to
stockholders for approval, including the election of our directors, amendments
to our certificate of incorporation, mergers, sales of assets and other
acquisitions or sales. We cannot assure you that these stockholders will not
exercise their influence over us in a manner detrimental to your interests. As
of May 9, 2001, Mr. Therrien holds approximately 5.8% of our common stock, M+W
Zander Holding GmbH, a subsidiary of Jenoptik AG, holds approximately 4.5% of
our common stock and Daifuku America Corporation, the U.S. affiliate of Daifuku
Co. Ltd. of Japan, holds approximately 1.6% of our common stock. Collectively,
these stockholders hold approximately 11.9% of our outstanding common stock.

On September 30, 1999 we entered into a stockholders agreement with Mr.
Therrien, M+W Zander Holding GmbH and Jenoptik AG. This agreement was amended on
October 16, 2000. Under the amended agreement, M+W Zander Holding GmbH agreed to
vote all of its shares on all matters in accordance with the recommendation of a
majority of our board of directors.

On January 6, 2000, in connection with our acquisition of Auto-Soft
Corporation and AutoSimulations, Inc. from Daifuku America Corporation, we
entered into a stockholders agreement with Daifuku America Corporation and
Daifuku Co., Ltd. Under the stockholders agreement, Daifuku agreed to vote all
of its shares of our common stock at each meeting of our stockholders in
accordance with the recommendation of our board of directors.

9
14

PROVISIONS OF OUR CERTIFICATE OF INCORPORATION, BYLAWS AND CONTRACTS MAY
DISCOURAGE TAKEOVER OFFERS AND MAY LIMIT THE PRICE INVESTORS WOULD BE WILLING TO
PAY FOR OUR COMMON STOCK.

Our certificate of incorporation and bylaws contain provisions that may make
an acquisition of us more difficult and discourage changes in our management.
These provisions could limit the price that certain investors might be willing
to pay in the future for shares of our common stock. In addition, we have
adopted a rights plan. In many potential takeover situations, rights issued
under the plan become exercisable to purchase our common stock at a price
substantially discounted from the then applicable market price of our common
stock. Because of its possible dilutive effect to a potential acquiror, the
rights plan would generally discourage third parties from proposing a merger
with or initiating a tender offer for us that is not approved by our board of
directors. Accordingly, the rights plan could have an adverse impact on our
stockholders who might want to vote in favor of the merger or participate in the
tender offer. In addition, shares of our preferred stock may be issued upon
terms the board of directors deems appropriate without stockholder approval. Our
ability to issue preferred stock in such a manner could enable our board of
directors to prevent changes in our management or control.

BECAUSE OF OUR SUBSTANTIAL INDEBTEDNESS, WE MAY BE UNABLE TO ADJUST OUR STRATEGY
TO MEET CHANGING CONDITIONS IN THE FUTURE.

As of June 30, 2001, we had long-term debt obligations of approximately $175
million due to the issuance of our 4.75% convertible subordinated notes on May
23, 2001. Our substantial debt may have important consequences for our future
operations. For instance, due to our debt:

- we may be unable to obtain additional future financing for capital
expenditures, acquisitions or general corporate purposes;

- we may be unable to withstand changing competitive pressures, economic
conditions or government regulations; and

- we may be unable to otherwise take advantage of significant business
opportunities that may arise.

10
15

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This prospectus and the documents we have filed with the Securities and
Exchange Commission which we have referenced on page 15 contain forward-looking
statements within the meaning of Section 27A of the Securities Act. These
statements involve known and unknown risks, uncertainties and other factors
which may cause our or our industry's actual results, performance or
achievements to be materially different from any future results, performance or
achievements expressed or implied by the forward-looking statements.
Forward-looking statements include, but are not limited to statements regarding:

- market acceptance of new products;

- competition in the industry;

- the ability to satisfy demand for our products;

- exchange rate fluctuations;

- the availability of debt and equity financing;

- the development of new competitive technologies;

- the availability of key components for our products;

- future acquisitions;

- the availability of qualified personnel;

- international, national, regional and local economic and political
changes;

- general economic conditions; and

- trends affecting the semiconductor industry,our financial conditions or
results of operations.

In some cases, you can identify forward-looking statements by terms
such as "may," will," "should," "could," "would," "expects," "plans,"
"anticipates," "believes," "estimates," "projects," "predicts," "potential" and
similar expressions intended to identify forward-looking statements. These
statements reflect our current views with respect to future events and are based
on assumptions and subject to risks and uncertainties. Given these
uncertainties, you should not place undue reliance on these forward-looking
statements. We discuss many of these risks in greater detail under the heading
"Risk Factors." Also, these forward-looking statements represent our estimates
and assumptions only as of the date of this prospectus.

You should read this prospectus and the documents that we incorporate
by reference in this prospectus completely and with the understanding that our
actual future results may be materially different from what we expect. We may
not update these forward-looking statements, even though our situation may
change in the future. We qualify all of our forward-looking statements by these
cautionary statements.

11
16

USE OF PROCEEDS

We will not receive any proceeds from the sale of our common stock by
the selling stockholders.

SELLING STOCKHOLDERS

The first selling stockholder is KLA-Tencor Technologies Corporation, a
subsidiary of KLA-Tencor Corporation. KLA-Tencor Technologies Corporation
obtained its shares of common stock from us in exchange for the e-diagnostic
infrastructure assets of KLA-Tencor Technologies Corporation and KLA-Tencor
Corporation on June 26, 2001. For these assets (i) we issued to KLA-Tencor
Technologies 331,153 shares of our common stock, (ii) we are obligated to pay
$17 million on July 26, 2002, in the form of cash or shares of our common stock
or any combination thereof, in our discretion; and (iii) we are obligated to
make payments contingent on the achievement of certain business milestones, in
the form of cash or shares of our common stock or any combination thereof, in
our discretion. We issued the shares to KLA-Tencor Technologies Corporation
pursuant to an exemption from the registration requirements of the Securities
Act of 1933. Under the terms of the asset purchase agreement with this selling
stockholder and KLA-Tencor Corporation, we agreed to register the shares of
Brooks common stock acquired by KLA-Tencor Technologies Corporation in the
transaction unless KLA-Tencor Technologies Corporation could sell all such
shares in a single day pursuant to Rule 144 of the Securities Act of 1933. Under
the terms of the asset purchase agreement, we agreed to use reasonable efforts
to file such registration statement within 15 days after the closing and use
commercially reasonable efforts to cause such registration statement to become
effective, initially registering 331,153 shares of our common stock.

Also, on the closing date, we entered into an original equipment
manufacturer agreement with KLA-Tencor Corporation. The term of this agreement
is for ten years, during which time we agreed to sell certain e-diagnostic
software products to KLA-Tencor Corporation and agreed that KLA-Tencor
Corporation may act as an original equipment manufacturer, resell our
e-diagnostic products with its products to end-users and use our products to
provide services to end-users. Additionally, we agreed to adjust the terms and
conditions of the agreement, including but not limited to price, to the extent
necessary to ensure that the terms and conditions applicable to KLA-Tencor
Corporation in the purchase of our e-diagnostic products are at least as
favorable when considered as a package of rights as the terms and condition that
we offer to any of our other customers who purchase similar quantities of
software and services. KLA-Tencor Corporation has been and continues to be one
of our customers.

The second selling stockholder is Ben Mahy. Mr. Mahy acquired 13,741
shares of our common stock from us as partial consideration for our purchase of
all of the issued and outstanding capital stock of SimCon, N.V. We issued these
shares pursuant to an exemption from the registration requirements of the
Securities Act of 1933. We agreed to register the shares of our common stock
acquired by Mr. Mahy in the transaction. Pursuant to our agreement with Mr.
Mahy, we will issue additional shares of our common stock to him in May 2002.
Prior to our acquisition, SimCon, N.V. was a value-added reseller of our
simulation, scheduling, production analysis and dispatching software.

The other selling stockholders are listed on the table below. These
selling stockholders acquired shares of our common stock from us as
consideration for our purchase of all of the issued and outstanding capital
stock of CCS Technology, Inc. We issued these shares pursuant to an exemption
from the registration requirements of the Securities Act of 1933. Under the
terms of the purchase agreement with these selling stockholders, we agreed to
register the shares of our common stock acquired by them in the transaction.
Under the terms of the purchase agreement, we agreed to file an S-3 registration
statement, and use commercially reasonable efforts to cause such registration
statement to become effective.

Registration by the selling stockholders does not necessarily mean that
the selling stockholders will sell any or all of their shares.

12
17

The information with regard to each selling stockholder in the table
below is based upon information provided to us by each selling stockholder as of
July, 2001. The shares listed below represent the shares that each selling
stockholder currently beneficially owns and the number of shares each selling
stockholder indicated it plans to offer. Pursuant to the asset purchase
agreement with KLA-Tencor Technologies Corporation and KLA-Tencor Corporation,
KLA-Tencor Technologies Corporation or KLA-Tencor Corporation may be issued
additional shares of common stock in the future. Pursuant to the stock purchase
agreement with Mr. Mahy, he will be issued additional shares of common stock in
the future. Each selling stockholder is subject to restrictions on the transfer
of its shares imposed by federal securities laws and by the agreement it
made with us.

The shares of common stock offered by this prospectus may be offered
from time to time by the selling stockholders named below:

Shares beneficially
Shares beneficially owned owned and ownership
and ownership percentage Number of shares being percentage after
Selling Stockholder prior to offering offered offering
------------------- ------------------------ ------------------------ -------------------

KLA-Tencor Technologies Corporation 331,153 (1.8%) 331,153 0 (0%)
Ben Mahy 13,741 (0.1%) 13,741 0 (0%)
Keith Peden 17,844 (0.1%) 17,844 0 (0%)
David Walsh 17,844 (*) 17,844 0 (0%)
Ronald Ham 9,111 (*) 9,111 0 (0%)
CEI 7,848 (*) 7,848 0 (0%)
Raymond Ritter 5,313 (*) 5,313 0 (0%)
William Fellinger 3,798 (*) 3,798 0 (0%)
Janet Stewart 3,798 (*) 3,798 0 (0%)
Merritt & Merritt 3,798 (*) 3,798 0 (0%)
Jocelyn Bolick 3,037 (*) 3,037 0 (0%)
Lauren Trono 2,276 (*) 2,276 0 (0%)
Norbert Lavigne 1,523 (*) 1,523 0 (0%)
Guy Davis 1,523 (*) 1,523 0 (0%)
James Dunn 762 (*) 762 0 (0%)
* Less than 0.05%

13
18

PLAN OF DISTRIBUTION

We are registering the shares on behalf of the selling stockholders.
"Selling stockholders" as used in this prospectus, include donees and pledgees
selling shares received from each named selling stockholder after the date of
this prospectus. The selling stockholders may offer the shares of Brooks common
stock at various times in one or more of the following transactions:

- on one or more exchange;

- in the over the counter market;

- in private transactions other than an exchange or in the over-the counter
market;

- in connection with short sales of the shares of Brooks common stock;

- by pledge to secure debts and other obligations;

- in connection with the writing of non-traded and exchange-traded call
options,

- in hedge transactions and in settlement of other transactions or over-the
counter options; or

- in a combination of any of the above transactions.

These transactions may include block transactions or crosses. Crosses
are transactions in which the same broker acts as an agent on both sides of the
trade.

The selling stockholders may sell their shares at market prices
prevailing at the time of sale, at prices related to such prevailing market
prices, or at negotiated or fixed prices.

The selling stockholders may use broker-dealers to sell their shares.
The selling stockholders may pay broker-dealers compensation in the form of
commissions, discounts or concessions in amounts to be negotiated in connection
with the sales. These broker-dealers and any other participating broker-dealers
may be deemed to be "underwriters" within the meaning of the Securities Act of
1933, as amended, in connection with such sales and any such commissions,
discount or concession may be deemed to be underwriting discounts or commissions
under the Act. If any of the selling stockholders was deemed an underwriter,
that selling stockholder might be subject to certain statutory liabilities,
including, but not limited to, Sections 11, 12 and 17 of the Securities Act and
Rule 10b-5 under the Exchange Act.

We have agreed to bear certain expenses of registration of the common
stock under the federal and state securities laws. These expenses include
registration and qualification fees, legal fees and expenses, and auditing and
accounting expenses. The selling stockholders have agreed to bear their own
counsel fees or any brokers' commissions or underwriting discounts incurred in
connection with the registration of their shares. The selling stockholders may
agree to indemnify any broker-dealer, agent or other person that participates in
transactions involving sales of the shares against liabilities, including
liabilities arising under the Securities Act of 1933, as amended.

The selling stockholders also may resell all or a portion of the shares
in open market transactions in reliance upon Rule 144 under the Securities Act
of 1933, as amended, rather than pursuant to this prospectus provided they meet
the criteria and conform to the requirements of that Rule.

There can be no assurance that the selling stockholders will sell any
or all of the shares of Brooks common stock offered hereunder.

The selling stockholders and any other person participating in such
distribution will be subject to the Exchange Act. The Exchange Act rules
include, without limitation, Regulation M, which may limit the timing of
purchases and sales of any common stock by selling stockholders and any other
such person. In addition, Regulation M of the Exchange Act may restrict the
ability of any person engaged in the distribution of the common stock to engage
in market-making activities with respect to the common stock being distributed
for a period of up to five business days prior to the commencement of such
distribution. This may affect the marketability of the common stock and the
ability of any person or entity to engage in market-making activities with
respect to the common stock.

14
19

Pursuant to the asset purchase agreement relating to our acquisition of
assets from KLA-Tencor Corporation and KLA-Tencor Technologies Corporation, we
and KLA-Tencor Technologies Corporation will be indemnified by each other
against certain liabilities, including certain liabilities under the Securities
Act or will be entitled to contribution in connection with these liabilities.
Pursuant to the stock purchase agreement relating to our acquisition of CCS
Technology, Inc., we and each selling stockholder who acquired shares of our
common stock pursuant to the stock purchase agreement will be indemnified by
each other against certain liabilities, including certain liabilities under the
Securities Act or will be entitled to contribution in connection with these
liabilities.

LEGAL MATTERS

The validity of the shares of common stock to be sold in this offering
will be passed upon for us by Brown, Rudnick, Freed & Gesmer, Boston,
Massachusetts.

EXPERTS

The audited financial statements incorporated in this prospectus by
reference to the Annual Report on Form 10-K of Brooks Automation, Inc. for the
year ended September 30, 2000, except as they relate to Irvine Optical Company,
LLC as of December 31, 1999 and for each of the two years in the period ended
December 31, 1999, have been audited by PricewaterhouseCoopers LLP, independent
accountants, and insofar as they relate to Irvine Optical Company, LLC as of
December 31, 1999 and for each of the two years in the period ended December 31,
1999, by Ernst & Young LLP, independent auditors, whose report thereon is
incorporated herein. Such financial statements have been so incorporated in
reliance in the reports of such independent accountants and independent auditors
given on the authority of such firms as experts in auditing and accounting.

The audited supplementary financial statements incorporated in this
prospectus by reference to the Current Report on Form 8-K dated August 20, 2001,
except as they relate to Irvine Optical Company, LLC as of December 31, 1999 and
for each of the two years in the period ended December 31, 1999 and Progressive
Technologies, Inc., as of December 31, 2000 and 1999 and for each of the three
years in the period ended December 31, 2000, have been audited by
PricewaterhouseCoopers LLP, independent accountants, and, insofar as they relate
to Irvine Optical Company, LLC as of December 31, 1999 and for each of the two
years in the period ended December 31, 1999 and Progressive Technologies, Inc.,
by Ernst & Young LLP, independent auditors and Arthur Andersen LLP, independent
public accountants, respectively, whose reports thereon are also incorporated
herein. Such supplementary financial statements have been so incorporated in
reliance on the reports of such independent accountants, independent auditors,
and independent public accountants given on the authority of such firms as
experts in auditing and accounting.

The audited financial statements of Auto-Soft Corporation and
AutoSimulations, Inc., incorporated in this prospectus by reference to Brooks
Automation, Inc.'s Current Report on Form 8-K/A, Amendment No. 1 to the Current
Report, dated February 14, 2000, have been so incorporated in reliance on the
reports of PricewaterhouseCoopers LLP, independent accountants, given on the
authority of said firm as experts in auditing and accounting.

Ernst & Young LLP, independent auditors, have audited the financial
statements of Irvine Optical Company, LLC as of December 31, 1999 and 1998, and
for the years then ended, as set forth in their report (which contains an
explanatory paragraph describing conditions that raise substantial doubt about
Irvine Optical Company, LLC's ability to continue as a going concern as
described in Note 1 to those financial statements). We have incorporated by
reference Ernst & Young LLP's report with respect to Irvine Optical Company,
LLC's financial statements in this prospectus and elsewhere in the registration
statement in reliance on Ernst & Young LLP's report, given on their authority as
experts in accounting and auditing.

Arthur Andersen LLP, as independent public accountants, has audited the
consolidated financial statements of Progressive Technologies, Inc. as of
December 31, 2000 and 1999 and for the three years then ended (not presented
separately herein), as indicated in their report with respect thereto. We have
incorporated by reference Arthur Andersen LLP's report with respect to
Progressive Technologies, Inc.'s consolidated financial statements in this
prospectus and elsewhere in the registration statement in reliance upon the
authority of Arthur Andersen LLP as experts in accounting and auditing in giving
said report.

WHERE YOU CAN FIND MORE INFORMATION

We are a reporting company and file annual, quarterly and current
reports, proxy statements and other information with the Securities and Exchange
Commission (SEC). You may read and copy these reports, proxy statements and
other information at the SEC's public reference rooms at 450 Fifth Street, NW.,
Washington, D.C., and in New York, NY and Chicago, IL. You can request copies of
these documents by writing to the SEC and paying a fee for the copying cost.
Please call the SEC at 1-800-SEC-0330 for more information about the operation
of the public reference rooms. Our SEC filings are also available at the SEC's
web site at http://www.sec.gov. In addition, you can read and copy our SEC
filings at the office of the National Association of Securities Dealers, Inc. at
1735 "K" Street, Washington, DC 20006.

We have filed with the SEC a registration statement on Form S-3 under
the Securities Act with respect to common stock offered in connection with this
prospectus. This prospectus does not contain all of the information set forth in
the registration statement. We have omitted certain parts of the registration
statement in accordance with the rules and regulations of the SEC. For further
information with respect to us and the common stock, you should refer to the
registration statement. Statements contained in this prospectus as to the
contents of any contract or other document are not necessarily complete and, in
each instance, you should refer to the copy of such contract or document filed
as an exhibit to or incorporated by reference in the registration statement.
Each statement as to the contents of such contract or document is qualified in
all respects by such reference. You may obtain copies of the registration
statement from the SEC's principal office in Washington, D.C. upon payment of
the fees prescribed by the SEC, or you may examine the registration statement
without charge at the offices of the SEC described above.

The SEC allows us to "incorporate by reference" information that we
file with it, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by

15
20
reference is an important part of this prospectus, and information that we file
later with the SEC will automatically update and supersede this information. We
incorporate by reference the documents listed below and any future filings we
will make with the SEC under Section 13(a), 13(c), 14 or 15(d) of the Exchange
Act until each selling stockholder sells all of its Brooks common stock:

- Annual Report on Form 10-K for the year ended September 30, 2000;

- Quarterly Reports on form 10-Q for the period ended December 31, 2000,
March 31, 2001, and June 30, 2001;

- Our definitive proxy materials on Schedule 14A as filed with the SEC on
January 24, 2001;

- The description of the common stock contained in our Registration
Statements on Form 8-A, as filed on January 24, 1995 and August 7,
1997; and

- Current Reports on Form 8-K and 8-K/A filed with the SEC on December 14,
1999, February 14, 2000, March 1, 2001; May 15, 2001; May 24, 2001; May
29, 2001; July 9, 2001; July 24, 2001 and August 21, 2001.

You may request a copy of these filings at no cost by writing or
telephoning us at the following address:

Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, Massachusetts 01824
Attention: Investor Relations
(978) 262-2400

You should rely only on the information or representations provided in
this prospectus. We have authorized no one to provide you with different
information. We are not making an offer of these securities in any state where
the offer is not permitted. You should not assume that the information in this
prospectus is accurate as of any date other than the date on the front of the
document.

16
21

PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION

SEC Registration Fee............................................................................... $4,709.98
Nasdaq National Market Listing Fee................................................................. $4,233.69
Printing Expenses.................................................................................. $10,000.00*
Accounting Fees and Expenses....................................................................... $10,000.00*
Legal Fees and Expenses............................................................................ $15,000.00*
Miscellaneous...................................................................................... $1,056.33
----------
TOTAL $45,000.00
==========

--------------------------------------------------------------------------------
* Estimated

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS

Article Ninth of our Certificate of Incorporation eliminates the personal
liability of our directors and stockholders for monetary damages for breach of
fiduciary duty to the full extent permitted by Delaware law. Article VII of our
Bylaws provides that we may indemnify our officers and directors to the fullest
extent permitted by the Delaware General Corporation Law. Section 145 of the
Delaware General Corporation Law authorizes a corporation to indemnify
directors, officers and employees unless such party has been adjudicated in any
proceeding not to have acted in good faith in the reasonable belief that his
action was in the best interest of the corporation. We also maintain directors
and officers liability insurance.

ITEM 16. EXHIBITS

EXHIBIT
NUMBER TITLE REFERENCE
------ ----- ---------

2.01 Agreement and Plan of Merger relating to the combination of AutoSimulations, Inc. and A*
Auto-Soft Corporation with the Registrant, dated January 6, 2000.

2.02 Interests for Stock Purchase Agreement relating to the acquisition of Irvine Optical G*
Company LLC by the Registrant dated May 5, 2000, as amended.

2.03 Stock for Cash Purchase Agreement relating to the acquisition of Hanyon Tech. Co., Ltd. B*
by the Registrant.

2.04 Assets for Cash Purchase Agreement relating to the acquisition of substantially all the C*
assets of Domain Manufacturing Corporation and its Subsidiary Domain Manufacturing SARL
by the Registrant.

2.05 Agreement and Plan of Merger relating to the combination of Smart Machines Inc. with the D*
Registrant.

2.06 Master Purchase Agreement relating to the acquisition of substantially all of the assets E*
of the Infab Division of Jenoptik by the Registrant.

2.07 Agreement and Plan of Merger relating to the combination of FASTech Integration, Inc. H*
with the Registrant.

2.08 Stock Purchase Agreement relating to the acquisition of SEMY Engineering, Inc. by the I*
Registrant.

2.09 Asset Purchase Agreement relating to the acquisition of assets of the e-diagnostic K*
infrastructure of KLA-Tencor Corporation and its subsidiary KLA-Tencor Technologies
Corporation.

2.10 Agreement and Plan of Merger relating to the combination of Progressive Technologies, M*
Inc. with the Registrant, dated June 27, 2001

4.01 Specimen Certificate for shares of the Registrant's common stock. F*

4.02 Description of Capital Stock (contained in the Certificate of Incorporation of the F*
Registrant, filed as Exhibit 3.01).

II-1
22

4.03 Registration Rights Agreement dated January 6, 2000. A*

4.04 Stockholders Agreement by and among the Registrant and Daifuku America Corporation dated A*
January 6, 2000.

4.05 Stockholders Agreement by and among the Company, Jenoptik AG, M+W Zander Holding GmbH E*
and Robert J. Therrien.

4.06 Indenture dated as of May 23, 2001 between Brooks and State Street Bank and Trust J*
Company (as Trustee).

4.07 Registration Rights Agreement dated May 23, 2001 among the Company and Credit Suisse J*
First Boston Corporation and SG Cowen Securities Corporation (as representatives of
several purchases).

4.08 Form of 4.75% Convertible Subordinated Note of the Company in the principal amount of J*
$175,000,000.00 dated as of May 23, 2001.

4.09 Rights Agreement between the Registrant and Bank Boston, N.A. as Rights Agent L*

4.10 Stock Purchase Agreement relating to the acquisition of CCS Technology, Inc. by the
Registrant. N*

5.01 Opinion of Brown, Rudnick, Freed & Gesmer. Filed
herewith

23.01 Consent of PricewaterhouseCoopers LLP, Independent Accountants. Filed
herewith

23.02 Consent of Ernst & Young LLP, Independent Auditors. Filed
herewith

23.03 Consent of Brown, Rudnick, Freed & Gesmer (included on Exhibit 5.01). Filed
herewith

23.04 Consent of Dr. Ebner, Dr. Stoltz and Partner GmbH. Filed
herewith

23.05 Consent of Arthur Andersen LLP, Independent Public Accountants. Filed
herewith

24.01 Power of Attorney (included on signature page of this Registration Statement). Filed
herewith

A. Incorporated by reference to our current report on Form 8-K filed on January
19, 2000 and amended on February 14, 2000.

B. Incorporated by reference to the Company's current report on Form 8-K filed
on May 6, 1999.

C. Incorporated by reference to the Company's current report on Form 8-K filed
on July 14, 1999.

D. Incorporated by reference to the Company's current report on Form 8-K filed
on September 15, 1999 and amended on September 29, 2000.

E. Incorporated by reference to the Company's current report on Form 8-K filed
on October 15, 1999.

F. Incorporated by reference to the Company's Registration Statement on Form
S-1 (Registration No. 33-87296). The number set forth herein is the number
of the Exhibit in said Registration Statement.

G. Incorporated by reference to the Company's Registration Statement on Form
S-3 (Registration No. 333-42620). The number set forth herein is the number
of the Exhibit in said Registration Statement.

H. Incorporated by reference to the Company's current report on Form 8-K filed
on October 15, 1998.

I. Incorporated by reference to the Company's current report on Form 8-K filed
on March 1, 2001.

J. Incorporated by reference to the Company's current report on Form 8-K filed
on May 29, 2001.

K. Incorporated by reference to the Company's current report on Form 8-K filed
on July 9, 2001.

L. Incorporated by reference to our Form 8-A filed on August 7, 1997.

M. Incorporated by reference to our current report on Form 8-K filed on July
24, 2001.

N. Incorporated by reference to the Company's Registration Statement on Form
S-8 (Registration No. 333-67432). The number set forth herein is the number
of the Exhibit in said Registration Statement.

* In accordance with Rule 12b-32 under the Securities Exchange Act of 1934, as
amended, reference is made to the documents previously filed with the
Securities and Exchange Commission, which documents are hereby incorporated
by reference.

ITEM 17. UNDERTAKINGS

Insofar as indemnification for liabilities arising under the Securities Act
of 1933, as amended, may be permitted to directors, officers and controlling
persons of the Registrant, pursuant to Item 15 above, the Registrant has been
advised that in the opinion of the Securities and Exchange Commission such
indemnification is against public policy as expressed in the Securities Act, and
is, therefore, unenforceable. In the event that a claim for indemnification
against such liabilities (other than the payment by the Registrant of expenses
incurred or paid by a
II-2
23
director, officer or controlling person of the Registrant in the successful
defense of any action, suit or proceeding) is asserted by such director, officer
or controlling person in connection with the securities being registered, the
Registrant will, unless in the opinion of its counsel the matter has been
settled by controlling precedent, submit to a court of appropriate jurisdiction
the question whether such indemnification by it is against public policy as
expressed in the Securities Act and will be governed by the final adjudication
of such issue.

The undersigned Registrant hereby further undertakes:

(1) To file, during any period in which offers or sales are being made, a
post-effective amendment to this Registration Statement: (i) to include
any prospectus required by section 10(a)(3) of the Securities Act; (ii)
to reflect in the prospectus any facts or events arising after the
effective date of the registration statement (or the most recent
post-effective amendment thereof) which, individually or in the
aggregate, represent a fundamental change in the information set forth
in the registration statement and (iii) to include any material
information with respect to the plan of distribution not previously
disclosed in the registration statement or any material change to such
information in the registration statement; provided however, that
clauses (i) and (ii) do not apply if the information required to be
included in a post-effective amendment by such clauses is contained in
periodic reports filed with or furnished to the Securities and Exchange
Commission by the Registrant pursuant to Section 13 or Section 15(d) of
the Securities Exchange Act of 1934 that are incorporated herein by
reference.

(2) That, for the purpose of determining any liability under the Securities
Act, each such post-effective amendment shall be deemed to be a new
registration statement relating to the securities offered therein, and
the offering of such securities at that time shall be deemed to be the
initial bona fide offering thereof.

(3) To remove from registration by means of a post-effective amendment any
of the securities being registered which remain unsold at the
termination of the offering.

(4) That, for purposes of determining any liability under the Securities
Act, each filing of the Registrant's annual report pursuant to section
13(a) or Section 15(d) of the Securities Exchange Act of 1934 that is
incorporated by reference in the registration statement shall be deemed
to be a new registration statement relating to the securities offered
therein, and the offering of such securities at that time shall be
deemed to be the initial bona fide offering thereof.

II-3

SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the
Registrant certifies that it has reasonable grounds to believe that it meets all
the requirements for filing on Form S-3 and has duly caused this Registration
Statement on Form S-3 to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Boston, Commonwealth of Massachusetts, on the
21st day of August, 2001.

BROOKS AUTOMATION, INC.

By: /s/ Robert J. Therrien
-----------------------------------
Robert J. Therrien
Chief Executive Officer and President

POWER OF ATTORNEY

KNOW ALL MEN BY THESE PRESENTS that each person whose signature appears
below constitutes and appoints Robert J. Therrien and Ellen B. Richstone, and
each of them, with the power to act without the other, his true and lawful
attorney-in-fact and agent, with full power of substitution and resubstitution
for him or in his name, place and stead, in any and all capacities to sign any
and all amendments or post-effective amendments to this Registration Statement,
and to file the same, with all exhibits thereto, and other documents in
connection therewith, and in connection with any registration of additional
securities pursuant to Rule 462(b) under the Securities Act of 1933, as amended,
to sign any abbreviated registration statements and any and all amendments
thereto, and to file the same, with all exhibits thereto and other documents in
connection therewith, in each case, with the Securities and Exchange Commission,
granting unto said attorneys-in-fact and agents, and each of them, full power
and authority to do and perform each and every act and thing requisite or
necessary to be done in and about the premises, as fully to all intents and
purposes as he might or could do in person, hereby ratifying and confirming all
that said attorneys-in-fact and agents or any of them, or their or his
substitutes, may lawfully do or cause to be done by virtue hereof.

PURSUANT TO THE REQUIREMENTS OF THE SECURITIES ACT OF 1933, THIS
REGISTRATION STATEMENT HAS BEEN SIGNED BY THE FOLLOWING PERSONS IN THE
CAPACITIES AND ON THE DATES INDICATED.

SIGNATURE TITLE DATE
--------- ----- ----

/s/ Robert J. Therrien Director, Chief Executive Officer and President (Principal August 21, 2001
--------------------------- Executive Officer)
Robert J. Therrien

/s/ Ellen B. Richstone Senior Vice President Finance and Administration and Chief August 21, 2001
--------------------------- Financial Officer
Ellen B. Richstone (Principal Financial Officer)

/s/ Steven E. Hebert Principal Accounting Officer August 21, 2001
---------------------------
Steven E. Hebert

/s/ Roger D. Emerick Director August 21, 2001
---------------------------
Roger D. Emerick

/s/ Amin J. Khoury Director August 21, 2001
----------------------------
Amin J. Khoury

/s/ Juergen Giessmann Director August 21, 2001
---------------------------
Juergen Giessmann

/s/ Joseph Martin Director August 21, 2001
---------------------------
Joseph Martin

II-4

EXHIBIT INDEX

EXHIBIT
NUMBER TITLE REFERENCE