content: <PAGE>
  
        As filed with the Securities and Exchange Commission on June 30, 2004
  
                                                            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. 1995 EMPLOYEE STOCK PURCHASE PLAN
              ---------------------------------------------------------
                              (Full Title of the Plan)
  
                     ROBERT J. THERRIEN, 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
  
  <TABLE>
  <CAPTION>
                                                                         Proposed
   Title of Each                                                         Maximum
      Class of                                   Proposed Maximum       Aggregate
  Securities to be         Amount to be           Offering Price         Offering
     Registered             Registered             Per Share(1)          Price(1)               Amount of Registration fee
     ----------            ------------          ----------------       ----------              --------------------------
  <S>                      <C>                   <C>                    <C>                     <C>
  Common Stock,            750,000 (2)               $19.59             $14,692,500                     $1,861.54
  $.01 par value           shares
  
  Preferred Share           750,000                    ----                    ----                          ----
  Purchase Rights (3)
  </TABLE>
  
  (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 of the high and low prices for the Registrant's common stock
        on the Nasdaq National Market on June 28, 2004.
  
  (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.
  
  (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
  
  <PAGE>
  
        of common stock issuable upon exercise of options granted or to be granted
        under the Registrant's 1995 Employee Stock Purchase 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.
  
                  STATEMENT REGARDING PRIOR REGISTRATION STATEMENTS
  
  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 the Registrant's 1995 Employee Stock Purchase Plan, an employee
  benefit plan, is effective. Pursuant to General Instruction E of Form S-8, this
  Registration Statement incorporates by reference the following registration
  statements filed by Registrant on Form S-8: Registration No. 333-40848,
  Registration No. 333-66457, Registration No. 333-66429, Registration No.
  333-07315, and Registration No. 333-88160, relating to an aggregate of 1,500,000
  shares issuable under the Registrant's 1995 Employee Stock Purchase Plan.
  Following the registration of the additional 750,000 shares under this
  Registration Statement, a total of 2,250,000 shares will be registered under the
  1995 Employee Stock Purchase Plan, as amended.
  
                                       PART II
  
                 INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  
  ITEM 8. EXHIBITS.
  
  <TABLE>
  <CAPTION>
  Exhibit No.                        Description                                                    Reference
  ----------                         -----------                                                    ---------
  <S>           <C>                                                                               <C>
  5.01          Legal Opinion of Brown Rudnick Berlack Israels LLP.                               Filed herewith
  
  23.01         Consent of PricewaterhouseCoopers LLP (independent registered public
                accounting firm for the Registrant).                                              Filed herewith
  
  23.02         Consent of Brown Rudnick Berlack Israels LLP (included in its legal opinion
                filed as Exhibit 5.01 to this Registration Statement).                            Filed herewith
  
  24.01         Power of Attorney (included on the signature page of this Registration
                Statement).                                                                       Filed herewith
  
  99.01         Registrant's 1995 Employee Stock Purchase Plan, as amended.                       Filed herewith
  </TABLE>
  
  <PAGE>
  
                                     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
  30th day of June, 2004.
  
                                       BROOKS AUTOMATION, INC.
  
                                       By:  /s/ Robert J. Therrien
                                            -----------------------------
                                            Robert J. Therrien
                                            Chief Executive Officer
  
                                  POWER OF ATTORNEY
  
        KNOW ALL MEN BY THESE PRESENTS, that the person whose signature appears
  below constitutes and appoints Robert J. Therrien and Thomas S. Grilk, and each
  of them (with full power to each of them to act alone), his or her true and
  lawful attorneys-in-fact and agents, with full power of substitution and
  resubstitution, for him or her and in his or her 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 or she 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, Chairman and Chief            June 30, 2004
  ---------------------------------               Executive Officer (Principal
  Robert J. Therrien                              Executive Officer)
  
  /s/ Robert W. Woodbury, Jr.                     Senior Vice President and               June 30, 2004
  ---------------------------------               Chief Financial Officer
  Robert W. Woodbury, Jr.                         (Principal Financial and
                                                  Accounting Officer)
  
  /s/ Edward C. Grady                             Director, President and Chief           June 30, 2004
  ---------------------------------               Operating Officer
  Edward C. Grady
  
  /s/ Roger D. Emerick                            Director                                June 30, 2004
  ---------------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                              Director                                June 30, 2004
  ---------------------------------
  Amin J. Khoury
  
  /s/ A. Clinton Allen                            Director                                June 30, 2004
  ---------------------------------
  A. Clinton Allen
  </TABLE>
  
  <PAGE>
  
  <TABLE>
  <S>                                             <C>                                     <C>
  /s/ Joseph R. Martin                            Director                                June 30, 2004
  ---------------------------------
  Joseph R. Martin
  
  /s/ John K. McGillicuddy                        Director                                June 30, 2004
  ---------------------------------
  John K. McGillicuddy
  </TABLE>
  
  <PAGE>
  
                                  INDEX TO EXHIBITS
  
  <TABLE>
  <CAPTION>
  Exhibit No.                        Description                                                    Reference
  ----------                         -----------                                                    ---------
  <S>           <C>                                                                               <C>
  5.01          Legal Opinion of Brown Rudnick Berlack Israels LLP.                               Filed herewith
  
  23.01         Consent of PricewaterhouseCoopers LLP (independent registered public
                accounting firm for the Registrant).                                              Filed herewith
  
  23.02         Consent of Brown Rudnick Berlack Israels LLP (included in its legal opinion
                filed as Exhibit 5.01 to this Registration Statement).                            Filed herewith
  
  24.01         Power of Attorney (included on the signature page of this Registration
                Statement).                                                                       Filed herewith
  
  99.01         Registrant's 1995 Employee Stock Purchase Plan, as amended.                       Filed herewith
  </TABLE>
metadata_documents: [{"type": "S-8", "sequence": "1", "filename": "b51020basv8.txt", "description": "BROOKS AUTOMATION, INC.", "secsgml_size_bytes": 12071}]
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": "333-117029", "film-number": "04892037"}, "business-address": {"street1": "15 ELIZABETH DRIVE", "city": "CHELMSFORD", "state": "MA", "zip": "01824", "phone": "(978) 262-2400"}, "mail-address": {"street1": "15 ELIZABETH DRIVE", "city": "CHELMSFORD", "state": "MA", "zip": "01824"}, "former-company": [{"former-conformed-name": "BROOKS-PRI AUTOMATION INC", "date-changed": "20020514"}, {"former-conformed-name": "BROOKS AUTOMATION INC", "date-changed": "19941215"}]}
text: As filed with the Securities and Exchange Commission on June 30, 2004
  
                                                            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. 1995 EMPLOYEE STOCK PURCHASE PLAN
              ---------------------------------------------------------
                              (Full Title of the Plan)
  
                     ROBERT J. THERRIEN, 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
   Title of Each                                                         Maximum
      Class of                                   Proposed Maximum       Aggregate
  Securities to be         Amount to be           Offering Price         Offering
     Registered             Registered             Per Share(1)          Price(1)               Amount of Registration fee
     ----------            ------------          ----------------       ----------              --------------------------
  Common Stock,            750,000 (2)               $19.59             $14,692,500                     $1,861.54
  $.01 par value           shares
  
  Preferred Share           750,000                    ----                    ----                          ----
  Purchase Rights (3)
  (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 of the high and low prices for the Registrant's common stock
        on the Nasdaq National Market on June 28, 2004.
  
  (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.
  
  (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 1995 Employee Stock Purchase 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.
  
                  STATEMENT REGARDING PRIOR REGISTRATION STATEMENTS
  
  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 the Registrant's 1995 Employee Stock Purchase Plan, an employee
  benefit plan, is effective. Pursuant to General Instruction E of Form S-8, this
  Registration Statement incorporates by reference the following registration
  statements filed by Registrant on Form S-8: Registration No. 333-40848,
  Registration No. 333-66457, Registration No. 333-66429, Registration No.
  333-07315, and Registration No. 333-88160, relating to an aggregate of 1,500,000
  shares issuable under the Registrant's 1995 Employee Stock Purchase Plan.
  Following the registration of the additional 750,000 shares under this
  Registration Statement, a total of 2,250,000 shares will be registered under the
  1995 Employee Stock Purchase Plan, as amended.
  
                                       PART II
  
                 INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  
  ITEM 8. EXHIBITS.
  Exhibit No.                        Description                                                    Reference
  ----------                         -----------                                                    ---------
  5.01          Legal Opinion of Brown Rudnick Berlack Israels LLP.                               Filed herewith
  
  23.01         Consent of PricewaterhouseCoopers LLP (independent registered public
                accounting firm for the Registrant).                                              Filed herewith
  
  23.02         Consent of Brown Rudnick Berlack Israels LLP (included in its legal opinion
                filed as Exhibit 5.01 to this Registration Statement).                            Filed herewith
  
  24.01         Power of Attorney (included on the signature page of this Registration
                Statement).                                                                       Filed herewith
  
  99.01         Registrant's 1995 Employee Stock Purchase Plan, as amended.                       Filed herewith
  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
  30th day of June, 2004.
  
                                       BROOKS AUTOMATION, INC.
  
                                       By:  /s/ Robert J. Therrien
                                            -----------------------------
                                            Robert J. Therrien
                                            Chief Executive Officer
  
                                  POWER OF ATTORNEY
  
        KNOW ALL MEN BY THESE PRESENTS, that the person whose signature appears
  below constitutes and appoints Robert J. Therrien and Thomas S. Grilk, and each
  of them (with full power to each of them to act alone), his or her true and
  lawful attorneys-in-fact and agents, with full power of substitution and
  resubstitution, for him or her and in his or her 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 or she 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, Chairman and Chief            June 30, 2004
  ---------------------------------               Executive Officer (Principal
  Robert J. Therrien                              Executive Officer)
  
  /s/ Robert W. Woodbury, Jr.                     Senior Vice President and               June 30, 2004
  ---------------------------------               Chief Financial Officer
  Robert W. Woodbury, Jr.                         (Principal Financial and
                                                  Accounting Officer)
  
  /s/ Edward C. Grady                             Director, President and Chief           June 30, 2004
  ---------------------------------               Operating Officer
  Edward C. Grady
  
  /s/ Roger D. Emerick                            Director                                June 30, 2004
  ---------------------------------
  Roger D. Emerick
  
  /s/ Amin J. Khoury                              Director                                June 30, 2004
  ---------------------------------
  Amin J. Khoury
  
  /s/ A. Clinton Allen                            Director                                June 30, 2004
  ---------------------------------
  A. Clinton Allen
  /s/ Joseph R. Martin                            Director                                June 30, 2004
  ---------------------------------
  Joseph R. Martin
  
  /s/ John K. McGillicuddy                        Director                                June 30, 2004
  ---------------------------------
  John K. McGillicuddy
  INDEX TO EXHIBITS
  Exhibit No.                        Description                                                    Reference
  ----------                         -----------                                                    ---------
  5.01          Legal Opinion of Brown Rudnick Berlack Israels LLP.                               Filed herewith
  
  23.01         Consent of PricewaterhouseCoopers LLP (independent registered public
                accounting firm for the Registrant).                                              Filed herewith
  
  23.02         Consent of Brown Rudnick Berlack Israels LLP (included in its legal opinion
                filed as Exhibit 5.01 to this Registration Statement).                            Filed herewith
  
  24.01         Power of Attorney (included on the signature page of this Registration
                Statement).                                                                       Filed herewith
  
  99.01         Registrant's 1995 Employee Stock Purchase Plan, as amended.                       Filed herewith