content: <PAGE>   1
       As filed with the Securities and Exchange Commission September 1, 2000
                                                          Registration No.
  ================================================================================
  
                         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               Amount to          Offering Price     Aggregate              Amount of
  to be Registered         be Registered      Per Share(1)       Offering Price(1)      Registration fee
  ----------------         -------------      --------------     -----------------      ----------------
  <S>                      <C>                <C>                <C>                    <C>
  Common Stock,            250,000(2)         $52.5625           $13,140,625.00         $3,469.13
  $.01 par value           shares
  
  Preferred Share          250,000            --                 --                      --
  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
  herein 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 August 30, 2000.
  
  (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 250,000 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.
  
  
                                        II-1
  <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 1st
  day of September, 2000.
  
                                            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        September 1, 2000
  -----------------------------           Officer and President
  Robert J. Therrien                      (Principal Executive Officer)
  
  /s/ Ellen B. Richstone                  Senior Vice President Finance    September 1, 2000
  -----------------------------           and Administration and Chief
  Ellen B. Richstone                      Financial Officer (Principal
                                          Financial Officer)
  
  /s/ Steven E. Hebert                    Principal Accounting Officer     September 1, 2000
  -----------------------------
  Steven E. Hebert
  
  /s/ Roger D. Emerick                    Director                         August 31, 2000
  -----------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                      Director                         September 1, 2000
  -----------------------------
  Amin J. Khoury
  
  /s/ Juergen Giessmann                   Director                         September 1, 2000
  -----------------------------
  Juergen Giessmann
  </TABLE>
                                        II-2
  <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.
  
  
                                        II-3
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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": "333-45092", "film-number": "715908"}, "business-address": {"street1": "15 ELIZABETH DRIVE", "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 September 1, 2000
                                                          Registration No.
  ================================================================================
  
                         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               Amount to          Offering Price     Aggregate              Amount of
  to be Registered         be Registered      Per Share(1)       Offering Price(1)      Registration fee
  ----------------         -------------      --------------     -----------------      ----------------
  Common Stock,            250,000(2)         $52.5625           $13,140,625.00         $3,469.13
  $.01 par value           shares
  
  Preferred Share          250,000            --                 --                      --
  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
  herein 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 August 30, 2000.
  
  (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 250,000 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.
  
                                        II-1
  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 1st
  day of September, 2000.
  
                                            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 1, 2000
  -----------------------------           Officer and President
  Robert J. Therrien                      (Principal Executive Officer)
  
  /s/ Ellen B. Richstone                  Senior Vice President Finance    September 1, 2000
  -----------------------------           and Administration and Chief
  Ellen B. Richstone                      Financial Officer (Principal
                                          Financial Officer)
  
  /s/ Steven E. Hebert                    Principal Accounting Officer     September 1, 2000
  -----------------------------
  Steven E. Hebert
  
  /s/ Roger D. Emerick                    Director                         August 31, 2000
  -----------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                      Director                         September 1, 2000
  -----------------------------
  Amin J. Khoury
  
  /s/ Juergen Giessmann                   Director                         September 1, 2000
  -----------------------------
  Juergen Giessmann
  II-2
  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.
  
                                        II-3