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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

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                                  SCHEDULE TO/A
                                  (RULE 13e-4)
            TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR 13(e)(1)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

                                (AMENDMENT NO. 2)

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                             BROOKS AUTOMATION, INC.
         (Name of Subject Company (Issuer) and Filing Person (Offeror))

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           OPTIONS TO PURCHASE COMMON STOCK, PAR VALUE $0.01 PER SHARE
                         (Title of Class of Securities)

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                                   114340 10 2
                      (CUSIP Number of Class of Securities)
                            (Underlying Common Stock)

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                               ROBERT J. THERRIEN
                             CHIEF EXECUTIVE OFFICER
                             BROOKS AUTOMATION, INC.
                               15 ELIZABETH DRIVE
                              CHEMLSFORD, MA 01824
                                 (978) 262-2400
   (Name, address and telephone number of person authorized to receive notices
                 and communications on behalf of filing person)

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                                   COPIES TO:
                             LAWRENCE M. LEVY, ESQ.
                        BROWN RUDNICK BERLACK ISRAELS LLP
                              ONE FINANCIAL CENTER
                                BOSTON, MA 02111
                                 (617) 856-8200

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                            CALCULATION OF FILING FEE

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        TRANSACTION VALUATION*                    AMOUNT OF FILING FEE**
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             $22,387,500                               $1,811.15
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*        Calculated solely for purposes of determining the filing fee. This
         amount assumes that options to purchase 6,375,954 shares of common
         stock of Brooks Automation, Inc. having an aggregate value of
         $22,387,500 as of January 29, 2003 will be exchanged and/or cancelled
         pursuant to this offer. The aggregate value of such options was
         calculated based on the Black-Scholes option pricing model. The amount
         of the filing fee, calculated in accordance with Rule 0-11(b) of the
         Securities Exchange Act of 1934, as amended, equals $80.90 per each $1
         million of the value of the transaction.

**       Previously paid.

[ ] Check box if any part of the fee is offset as provided by Rule 0-11(a)(2)
and identify the filing with which the offsetting fee was previously paid.
Identify the previous filing by registration statement number, or the Form or
Schedule and the date of its filing.

                       Amount Previously Paid: $1,811.15.
                     Form or Registration No.: Schedule TO.
                     Filing party: Brooks Automation, Inc.
                           Date filed: March 13, 2003.

[ ] Check box if the filing relates solely to preliminary communications made
before the commencement of a tender offer.

Check the appropriate boxes below to designate any transactions to which the
statement relates:

             [ ]    third party tender offer subject to Rule 14d-1.
             [X]    issuer tender offer subject to Rule 13e-4.
             [ ]    going-private transaction subject to Rule 13e-3.
             [ ]    amendment to Schedule 13D under Rule 13d-2.

Check the following box if the filing is a final amendment reporting the
results of the tender offer.  [ ]

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         This Amendment No. 2 amends and supplements the Tender Offer Statement
on Schedule TO filed by Brooks Automation, Inc. ("Brooks") with the Securities
and Exchange Commission on March 13, 2002, as amended by Amendment No. 1 filed
on March 24, 2003, relating to Brooks' offer to exchange certain outstanding
options to purchase shares of Brooks' common stock held by eligible employees
for new options to purchase shares of Brooks' common stock.


         This Amendment No. 2 accomplishes the following:

         1.       Filed herewith as Item 12(d)(6) is a reminder notice to
                  employees distributed via email on March 27, 2003.

                                       2



         2.       Filed herewith as Item 12(d)(7) is a Supplement to the Offer
                  to Exchange, dated March 27, 2003.


         All of the other terms of the Offer to Exchange remain unchanged.



ITEM 12. EXHIBITS.

         (a)
         (1)*     Offer to Exchange, dated March 13, 2003.

         (2)*     Memorandum from Robert J. Therrien, Chief Executive Officer
                  of the Company, dated March 13, 2003.

         (3)*     Frequently Asked Questions.

         (4)*     Election Form.

         (5)*     Notice to Withdraw from the Offer.

         (6)*     Brooks Automation, Inc. Annual Report on Form 10-K for its
                  fiscal year ended September 30, 2002, filed with the
                  Securities and Exchange Commission on December 30, 2002 and
                  incorporated herein by reference.

         (7)*     Brooks Automation, Inc. Quarterly Report on Form 10-Q for its
                  quarter ended December 31, 2002, filed with the Securities
                  and Exchange Commission on February 14, 2003 and incorporated
                  herein by reference.

         (b)      Not applicable.

         (c)      Not applicable.

         (d)
         (1)*     Stockholder Agreement dated September 30, 1999 by and among
                  the Company, Jenoptik AG, M&W Zander Holding GmbH and Robert
                  J. Therrien relating to the acquisition of substantially all
                  of the assets of the Infab Division of Jenoptik AG by the
                  Company, incorporated herein by reference to the Company's
                  current report on Form 8-K filed with the Securities Exchange
                  Commission on October 15, 1999.

         (2)*     Transitional Services Agreement dated September 30, 1999
                  between the Company and Jenoptik AG relating to the Company's
                  German manufacturing facility, incorporated herein by
                  reference to Exhibit 10.33 of the Company's Annual Report on
                  Form 10-K filed with the Securities Exchange Commission on
                  December 29, 1999 for the fiscal year ended September 30,
                  1999.

         (3)+     Brooks Automation, Inc. 1998 Employee Equity Incentive Plan.

         (4)*     Brooks Automation, Inc. 2000 Combination Stock Option Plan.

         (5)+     Reminder Notice to Employees.

         (6)      Reminder Notice to Employees, dated March 27, 2003.

         (7)      Supplement to the Offer to Exchange, dated March 27, 2003.

         (e)      Not applicable.

         (f)      Not applicable.

                                       3


         (g)      Not applicable.

         (h)      Not applicable.



*    Previously filed as an exhibit to the Schedule TO filed with the
     Securities and Exchange Commission on March 13, 2003.

+    Previously filed as an exhibit to the Amendment No. 1 to Schedule TO filed
     with the Securities and Exchange Commission on March 24, 2003.


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                                    SIGNATURE

         After due inquiry and to the best of my knowledge and belief, I certify
that the information set forth in this Amendment to the Schedule TO is true,
complete and correct.
                                           BROOKS AUTOMATION, INC.

                                           /s/ Lynda M. Avallone
                                           -------------------------------------
                                           Lynda M. Avallone
                                           Vice President, Corporate Treasurer

Date: March 27, 2003

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                                INDEX TO EXHIBITS

  Exhibit
   Number                               Description
  -------      -----------------------------------------------------------------

  (a)(1)*      Offer to Exchange, dated March 13, 2003.

  (a)(2)*      Memorandum from Robert J. Therrien, Chief Executive Officer of
               the Company, dated March 13, 2003.

  (a)(3)*      Frequently Asked Questions.

  (a)(4)*      Election Form.

  (a)(5)*      Notice to Withdraw from the Offer.

  (a)(6)*      Brooks Automation, Inc. Annual Report on Form 10-K for its
               fiscal year ended September 30, 2002, filed with the Securities
               and Exchange Commission on December 30, 2002 and incorporated
               herein by reference.

  (a)(7)*      Brooks Automation, Inc. Quarterly Report on Form 10-Q for its
               quarter ended December 31, 2002, filed with the Securities and
               Exchange Commission on February 14, 2003 and incorporated herein
               by reference.

  (d)(1)*      Stockholder Agreement dated September 30, 1999 by and among the
               Company, Jenoptik AG, M&W Zander Holding GmbH and Robert J.
               Therrien relating to the acquisition of substantially all of the
               assets of the Infab Division of Jenoptik AG by the Company,
               incorporated herein by reference to the

                                       4



               Company's current report on Form 8-K filed with the Securities
               Exchange Commission on October 15, 1999.

  (d)(2)*      Transitional Services Agreement dated September 30, 1999
               between the Company and Jenoptik AG relating to the Company's
               German manufacturing facility, incorporated herein by reference
               to Exhibit 10.33 of the Company's Annual Report on Form 10-K
               filed with the Securities Exchange Commission on December 29,
               1999 for the fiscal year ended September 30, 1999.

  (d)(3)+      Brooks Automation, Inc. 1998 Employee Equity Incentive Plan.

  (d)(4)*      Brooks Automation, Inc. 2000 Combination Stock Option Plan.

  (d)(5)+      Reminder Notice to Employees.

  (d)(6)       Reminder Notice to Employees, dated March 27, 2003.

  (d)(7)       Supplement to the Offer to Exchange, dated March 27, 2003.


*  Previously filed as an exhibit to the Schedule TO filed with the Securities
   and Exchange Commission on March 13, 2003.

+  Previously filed as an exhibit to the Amendment No. 1 to Schedule TO filed
   with the Securities and Exchange Commission on March 24, 2003.


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