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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                               -------------------

                                  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. 3)

                               -------------------

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

                               -------------------

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

                               -------------------

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

                               -------------------

                               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)

                               -------------------

                                   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. 3 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 and Amendment No. 2 filed on March 27, 2004, 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. 3 accomplishes the following:

      (i)   In the first paragraph, first sentence on page 1 of the Election
            Form filed as Exhibit (a)(4), representations made by employees
            completing the form that he or she has "read" and

                                       2

            "understood" the terms and conditions of the Offer are hereby
            deleted.

      (ii)  On page 1 of the Notice to Withdraw from the Offer filed as Exhibit
            (a)(5), the first and second sentences of the second paragraph are
            hereby deleted.


      Unless revised by Amendment No. 1 or Amendment No. 2 to the Schedule TO,
filed on March 24, 2003 and March 27, 2003, respectively, all of the other terms
of the Offer to Exchange remain unchanged.


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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/Robert W. Woodbury
                                      -----------------------------------
                                      Robert W. Woodbury
                                      Senior Vice President,
                                      Chief Financial Officer

Date: April 3, 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.

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

                                       3

(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.

(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.

++ Previously filed as an exhibit to the Amendment No. 2 to Schedule TO filed
   with the Securities and Exchange Commission on March 27, 2003.









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