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     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.

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(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.

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                                     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-
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                                   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


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                                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.