content: <PAGE>   1
       As filed with the Securities and Exchange Commission on March 30, 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)
  
  <TABLE>
  <CAPTION>
                                      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)            Offering Price     Registration fee
  -------------         -------------           ------------            --------------     ----------------
  <S>                   <C>                     <C>                     <C>                <C>
  Common Stock,         750,000(2)              $43.25                  $32,437,500        $8,109.38
  $.01 par value
  
  Preferred Share       750,000                 -----                   -----              -----
  Purchase Rights
  (3)
  =========================================================================================================
  </TABLE>
  
  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 March 27, 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.
  
  <PAGE>   2
  
  (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 750,000 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.
  
  <PAGE>   3
  
                                       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 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.
  
  
  
                                        -3-
  <PAGE>   4
  
                                     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
  27th day of March, 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.
  
  
  <TABLE>
  <CAPTION>
  Signature                               Title                            Date
  ---------                               -----                            ----
  
  <S>                                     <C>                              <C>
  /s/ Robert J. Therrien                  Director, Chief Executive        March 27, 2001
  ----------------------------------      Officer and President
  Robert J. Therrien                      (Principal Executive Officer)
  
  /s/ Ellen B. Richstone                  Senior Vice President Finance    March 27, 2001
  ----------------------------------      and Administration and Chief
  Ellen B. Richstone                      Financial Officer (Principal
                                          Financial Officer)
  
  /s/ Steven E. Hebert                    Principal Accounting Officer     March 27, 2001
  ----------------------------------
  Steven E. Hebert
  
  /s/ Roger D. Emerick                    Director                         March 27, 2001
  ----------------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                      Director                         March 27, 2001
  ----------------------------------
  Amin J. Khoury
  
  /s/ Juergen Giessmann                   Director                         March 27, 2001
  ----------------------------------
  Juergen Giessmann
  </TABLE>
  
  <PAGE>   5
  
                                  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 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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metadata_filer: {"company-data": {"conformed-name": "BROOKS AUTOMATION INC", "cik": "0000933974", "assigned-sic": "3559", "irs-number": "043040660", "state-of-incorporation": "DE", "fiscal-year-end": "0930"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-57974", "film-number": "1586614"}, "business-address": {"street1": "15 ELIZABETH DR", "city": "CHELMSFORD", "state": "MA", "zip": "01824", "phone": "9782622566"}, "mail-address": {"street1": "15 ELIZABETH DRIVE", "city": "CHELMSBORO", "state": "MA", "zip": "01824"}}
text: 1
       As filed with the Securities and Exchange Commission on March 30, 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)            Offering Price     Registration fee
  -------------         -------------           ------------            --------------     ----------------
  Common Stock,         750,000(2)              $43.25                  $32,437,500        $8,109.38
  $.01 par value
  
  Preferred Share       750,000                 -----                   -----              -----
  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 March 27, 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.
  2
  
  (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 750,000 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.
  3
  
                                       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 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.
  
                                        -3-
  4
  
                                     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
  27th day of March, 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        March 27, 2001
  ----------------------------------      Officer and President
  Robert J. Therrien                      (Principal Executive Officer)
  
  /s/ Ellen B. Richstone                  Senior Vice President Finance    March 27, 2001
  ----------------------------------      and Administration and Chief
  Ellen B. Richstone                      Financial Officer (Principal
                                          Financial Officer)
  
  /s/ Steven E. Hebert                    Principal Accounting Officer     March 27, 2001
  ----------------------------------
  Steven E. Hebert
  
  /s/ Roger D. Emerick                    Director                         March 27, 2001
  ----------------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                      Director                         March 27, 2001
  ----------------------------------
  Amin J. Khoury
  
  /s/ Juergen Giessmann                   Director                         March 27, 2001
  ----------------------------------
  Juergen Giessmann
  5
  
                                  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 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.