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     As filed with the Securities and Exchange Commission on October 3, 2001
                              Registration No. 333-
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM S-8

                             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, MA 01824
               (Address of Principal Executive Offices) (Zip Code)


                             BROOKS AUTOMATION, INC.
                       1998 EMPLOYEE EQUITY INCENTIVE PLAN
                            (Full Title of the Plan)

            ROBERT J. THERRIEN, PRESIDENT AND CHIEF EXECUTIVE OFFICER
                             BROOKS AUTOMATION, INC.
                               15 ELIZABETH DRIVE
                              CHELMSFORD, MA 01824
                     (Name and Address of Agent For Service)

                                 (978) 262-2400
          (Telephone Number, Including Area Code, of Agent For Service)




                                       CALCULATION OF REGISTRATION FEE
===========================================================================================================
                                             Proposed                 Proposed
Title of                                     Maximum                  Maximum
Securities to            Amount to           Offering Price           Aggregate            Amount of
be Registered            be Registered       Per Share(1)             Offerin Price(1)     Registration Fee
----------               -------------       --------------           ----------------     ----------------
                                                                                 
Common Stock,            500,000(2)            $25.68                 $12,840,000            $3,210.00
$.01 par value

Preferred Share          500,000                    --                         --                   --
Purchase Rights(3)
============================================================================================================


This Registration Statement relates to the registration of additional securities
of the same class as other securities for which a registration statement on this
form relating to an employee benefit plan is effective. Pursuant to General
Instruction E of Form S-8, the contents of the Registrant's registration
statement on Form S-8 (Registration No. 333-66455) are hereby incorporated by
reference.

(1)   Estimated solely for the purpose of determining the registration fee
      pursuant to Rule 457(h) under the Securities Act of 1933, on the basis of
      the average high and low prices for the Registrant's common stock on the
      Nasdaq National Market on October 2, 2001.

(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.

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(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 500,000 rights registered by
      this Registration Statement represent one right that may be issued in
      connection with each share of common stock issuable upon exercise of
      options granted or to be granted under the Registrant's 1998 Employee
      Equity Incentive Plan. 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.


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                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 8. EXHIBITS.

        4.2       Description of Capital Stock (contained in the Certificate of
                  Incorporation, as amended, of the Registrant, filed as Exhibit
                  3.01 to the Registrant's Quarterly Report on Form 10-Q).*

        4.3       Rights Agreement, dated July 23, 1997.**

        5.1       Legal Opinion of Brown, Rudnick, Freed & Gesmer.

        23.1      Consent of PricewaterhouseCoopers LLP

        23.2      Consent of Ernst & Young LLP, Independent Auditors

        23.3      Consent of Arthur Andersen LLP, Independent Public Accountants

        23.4      Consent of Brown, Rudnick, Freed & Gesmer (included in its
                  legal opinion filed as Exhibit 5.1 to this Registration
                  Statement).

        24        Power of Attorney (included on the signature page of this
                  Registration Statement).

        99.4      Registrant's 1998 Employee Equity Incentive Plan, as amended.*

        ---------
        * Incorporated by reference to the Registrant's Quarterly Report on Form
        10-Q for the quarterly period ended March 31, 2000. The number assigned
        to each Exhibit above is the same as the number assigned to the Exhibit
        in the Quarterly Report.

        ** Incorporated by reference to the Registrant's Registration Statement
        on Form S-1 (Registration No. 333-34487). The number assigned to the
        Exhibit above is the same as the number assigned to the Exhibit in the
        Registration Statement.



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                                   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
of the requirements for filing on Form S-8 and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the Town of Chelmsford, Commonwealth of Massachusetts, on the
28th day of September, 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 the person whose signature appears
below constitutes and appoints Robert J. Therrien and Ellen B. Richstone and
each of them (with full power to each of them to act alone), his true and lawful
attorneys-in-fact and agents, with full power of substitution and
resubstitution, for him and in his name, place and stead, in any and all
capacities, to sign any or all amendments (including post-effective amendments)
to this Registration Statement, and to file the same, with all exhibits thereto
and other documents in connection therewith, 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 and 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
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 date indicated.




SIGNATURE                                        TITLE                            DATE
---------                                        -----                            ----
                                                                            
/s/ Robert J. Therrien                           Director, Chief Executive        September 28, 2001
-------------------------------------
Robert J. Therrien                               Officer and President
                                                 (Principal Executive Officer)
/s/ Ellen B. Richstone                           Senior Vice President Finance    September 28, 2001
------------------------------------             and Administration and Chief
Ellen B. Richstone                               Financial Officer (Principal
                                                 Financial Officer)
/s/ Steven E. Hebert                             Principal Accounting Officer     September 28, 2001
-------------------------------------
Steven E. Hebert

/s/ Roger D. Emerick                             Director                         September 28, 2001
------------------------------------
Roger D. Emerick

/s/ Amin J. Khoury                               Director                         September 28, 2001
-----------------------------------
Amin J. Khoury

/s/ Juergen Giessmann                            Director                         September 28, 2001
------------------------------------
Juergen Giessmann

/s/ Joseph Martin                                Director                         September 28, 2001
------------------------------------
Joseph Martin



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                                INDEX TO EXHIBITS
EXHIBIT
NUMBER
-------
4.2       Description of Capital Stock (contained in the Certificate of
          Incorporation, as amended, of the Registrant, filed as Exhibit
          3.01 to the Registrant's Quarterly Report on Form 10-Q).*

4.3       Rights Agreement, dated July 23, 1997.**

5.1       Legal Opinion of Brown, Rudnick, Freed & Gesmer.

23.1      Consent of PricewaterhouseCoopers LLP.

23.2      Consent of Ernst & Young LLP, Independent Auditors

23.3      Consent of Arthur Andersen LLP, Independent Public Accountants

23.4      Consent of Brown, Rudnick, Freed & Gesmer (included in its legal
          opinion filed as Exhibit 5.1 to this Registration Statement).

24        Power of Attorney (included on the signature page of this
          Registration Statement).

99.4      Registrant's 1998 Employee Equity Incentive Plan, as amended.*

        ---------
        * Incorporated by reference to the Registrant's Quarterly Report on Form
        10-Q for the quarterly period ended March 31, 2000. The number assigned
        to each Exhibit above is the same as the number assigned to the Exhibit
        in the Quarterly Report.

        ** Incorporated by reference to the Registrant's Registration Statement
        on Form S-1 (Registration No. 333- 34487). The number assigned to the
        Exhibit above is the same as the number assigned to the Exhibit in the
        Registration Statement.