<PAGE>   1
                                                                 Exhibit 10.1

                                  $150,000,000

                             BROOKS AUTOMATION, INC.

              4.75% CONVERTIBLE SUBORDINATED NOTES DUE JUNE 1, 2008

                               PURCHASE AGREEMENT

                                  May 17, 2001


CREDIT SUISSE FIRST BOSTON CORPORATION
SG COWEN SECURITIES CORPORATION,
 As Representatives of the Several Purchasers,
  c/o Credit Suisse First Boston Corporation,
         Eleven Madison Avenue,
         New York, N.Y. 10010-3629

Dear Sirs:

         1. Introductory. Brooks Automation, Inc., a Delaware corporation (the
"COMPANY"), proposes, subject to the terms and conditions stated herein, to
issue and sell to the several initial purchasers named in Schedule A hereto (the
"PURCHASERS") U.S.$150,000,000 principal amount of its 4.75% Convertible
Subordinated Notes Due June 1, 2008 (the "FIRM SECURITIES") and also proposes to
grant to the Purchasers an option, exercisable from time to time by Credit
Suisse First Boston Corporation to purchase an aggregate of up to an additional
$25,000,000 principal amount ("OPTIONAL SECURITIES") of its 4.75% Convertible
Subordinated Notes Due June 1, 2008, each to be issued under an indenture, dated
as of May 23, 2001 (the "INDENTURE"), between the Company and State Street Bank
and Trust Company, as Trustee. The Firm Securities and the Optional Securities
which the Purchasers may elect to purchase pursuant to Section 3 hereof are
herein collectively called the "OFFERED SECURITIES". The United States
Securities Act of 1933 is herein referred to as the "SECURITIES ACT."

         The Company hereby agrees with the several Purchasers as follows:

         2. Representations and Warranties of the Company. The Company
represents and warrants to, and agrees with, the several Purchasers that:

                  (a) A preliminary offering circular and an offering circular
         relating to the Offered Securities to be offered by the Purchasers have
         been prepared by the Company. Such preliminary offering circular (the
         "PRELIMINARY OFFERING CIRCULAR") and offering circular (the "OFFERING
         CIRCULAR"), as supplemented as of the date of this Agreement, and any
         other document approved by the Company for use in connection with the
         contemplated resale of the Offered Securities are hereinafter
         collectively referred to as the "OFFERING DOCUMENT". On the date of
         this Agreement, the Offering Document does not include any untrue
         statement of a material fact or omit to state any material fact
         necessary in order to make the statements therein, in the light of the
         circumstances under which they were made, not misleading. The preceding
         sentence does not apply to statements in or omissions from the Offering
         Document based upon written information furnished to the Company by any
         Purchaser through Credit Suisse First Boston Corporation
<PAGE>   2
                           Purchase Agreement-Page 2


         ("CSFBC") specifically for use therein, it being understood and agreed
         that the only such information is that described as such in Section
         7(b) hereof. Except as disclosed in the Offering Document, on the date
         of this Agreement, the Company's Annual Report on Form 10-K most
         recently filed with the Securities and Exchange Commission (the
         "COMMISSION") and all subsequent reports (collectively, the "EXCHANGE
         ACT REPORTS") which have been filed by the Company with the Commission
         or sent to stockholders pursuant to the Securities Exchange Act of 1934
         (the "EXCHANGE ACT") do not include any untrue statement of a material
         fact or omit to state any material fact necessary to make the
         statements therein, in the light of the circumstances under which they
         were made, not misleading. Such documents, when they were filed with
         the Commission, conformed in all material respects to the requirements
         of the Exchange Act and the rules and regulations of the Commission
         thereunder.

                  (b) The Company has been duly incorporated and is an existing
         corporation in good standing under the laws of the State of Delaware,
         with power and authority (corporate and other) to own its properties
         and conduct its business as described in the Offering Document; and the
         Company is duly qualified to do business as a foreign corporation in
         good standing in all other jurisdictions in which its ownership or
         lease of property or the conduct of its business requires such
         qualification, except where such failure to so qualify would
         individually or in the aggregate have a material adverse effect on the
         condition (financial or other), business, properties or results of
         operations of the Company and its subsidiaries taken as a whole
         ("MATERIAL ADVERSE EFFECT").

                  (c) Each subsidiary of the Company has been duly incorporated
         and is an existing corporation in good standing under the laws of the
         jurisdiction of its incorporation, with power and authority (corporate
         and other) to own its properties and conduct its business as described
         in the Offering Document; and each subsidiary of the Company is duly
         qualified to do business as a foreign corporation in good standing in
         all other jurisdictions in which its ownership or lease of property or
         the conduct of its business requires such qualification except where
         such failure to so qualify would not have a Material Adverse Effect;
         excluding those subsidiaries of the Company set forth on Schedule B
         attached hereto ("MATERIAL SUBSIDIARIES"), the Company has no other
         subsidiaries as of the date hereof which (A) on an individual basis,
         have total assets or total revenues as of and for the fiscal year ended
         September 30, 2000, in each case as determined in accordance with
         generally accepted accounting principles ("GAAP"), in excess of ten
         percent (10%) of the Company's total assets or total revenues as
         reported on a consolidated basis as of and for the fiscal year ended
         September 30, 2000, or (B) in the aggregate, have total assets or total
         revenues as of and for the fiscal year ended September 30, 2000, as
         determined in accordance with GAAP, in excess of ten percent (10%) of
         the Company's total assets or total revenues as reported on a
         consolidated basis as of and for the fiscal year ended September 30,
         2000; all of the issued and outstanding capital stock of each
         subsidiary of the Company has been duly authorized and validly issued
         and is fully paid and nonassessable; and the capital stock of each
         subsidiary owned by the Company, directly or through subsidiaries, is
         owned free from liens, encumbrances and defects.

                  (d) The Indenture has been duly authorized; the Offered
         Securities have been duly authorized; and when the Offered Securities
         are delivered and paid for pursuant to this Agreement on each Closing
         Date (as defined below), the Indenture will have been duly executed and
         delivered, such Offered Securities will have been duly executed,
         authenticated, issued and delivered and will conform to the description
         thereof contained in the Offering Document and the Indenture and such
         Offered Securities will constitute valid and legally binding
         obligations of
<PAGE>   3
                           Purchase Agreement-Page 3

         the Company, enforceable in accordance with their terms, subject to
         bankruptcy, insolvency, fraudulent transfer, reorganization, moratorium
         and similar laws of general applicability relating to or affecting
         creditors' rights and to general equity principles.

                  (e) All outstanding shares of capital stock of the Company
         have been duly authorized, validly issued, fully paid and are
         nonassessable and conform to the description thereof contained in the
         Offering Document.

                  (f) When the Offered Securities are delivered and paid for
         pursuant to this Agreement on each Closing Date, such Offered
         Securities will be convertible into the shares of common stock
         ("UNDERLYING SHARES") of the Company in accordance with the terms of
         the Indenture; the Underlying Shares initially issuable upon conversion
         of such Offered Securities have been duly authorized and reserved for
         issuance upon such conversion and, when issued upon such conversion,
         will be validly issued, fully paid and nonassessable; the outstanding
         Underlying Shares have been duly authorized and validly issued, are
         fully paid and nonassessable and conform to the description thereof
         contained in the Offering Document; and the stockholders of the Company
         have no preemptive rights with respect to the Offered Securities or the
         Underlying Shares.

                  (g) No consent, approval, authorization, or order of, or
         filing with, any governmental agency or body or any court is required
         for the consummation of the transactions contemplated by this Agreement
         and the Registration Rights Agreement dated the date hereof, between
         the Company and the Purchasers (the "REGISTRATION RIGHTS AGREEMENT"),
         in connection with the issuance and sale of the Offered Securities by
         the Company except for the order of the Commission declaring the Self
         Registration Statement (as defined in the Registration Rights
         Agreement) effective.

                  (h) The execution, delivery and performance of the Indenture,
         this Agreement and the Registration Rights Agreement, and the issuance
         and sale of the Offered Securities and compliance with the terms and
         provisions thereof will not result in a breach or violation of any of
         the terms and provisions of, or constitute a default under, any
         statute, any rule, regulation or order of any governmental agency or
         body or any court, domestic or foreign, having jurisdiction over the
         Company or any subsidiary of the Company or any of their properties, or
         any agreement or instrument to which the Company or any such subsidiary
         is a party or by which the Company or any such subsidiary is bound or
         to which any of the properties of the Company or any such subsidiary is
         subject, or the charter or by-laws of the Company or any such
         subsidiary, and the Company has full power and authority to authorize,
         issue and sell the Offered Securities as contemplated by this
         Agreement.

                  (i) This Agreement and the Registration Rights Agreement have
         been duly authorized, executed and delivered by the Company and
         constitute a valid and legally binding obligation of the Company,
         enforceable in accordance with their respective terms, subject to
         bankruptcy, insolvency, fraudulent transfer, reorganization, moratorium
         and similar laws of general applicability relating to or affecting
         creditors' rights and to general equity principles.

                  (j) Except as disclosed in the Offering Document, the Company
         and its subsidiaries have good and marketable title to all real
         properties and all other properties and assets owned by them, in each
         case free from liens, encumbrances and defects that would materially
         affect the value thereof or materially interfere with the use made or
         to be made thereof by them; and except as
<PAGE>   4
                           Purchase Agreement-Page 4

         disclosed in the Offering Document, the Company and its subsidiaries
         hold any leased real or personal property under valid and enforceable
         leases with no exceptions that would materially interfere with the use
         made or to be made thereof by them.

                  (k) The Company and its subsidiaries possess adequate
         certificates, authorities or permits issued by appropriate governmental
         agencies or bodies necessary to conduct the business now operated by
         them and have not received any notice of proceedings relating to the
         revocation or modification of any such certificate, authority or permit
         that, if determined adversely to the Company or any of its
         subsidiaries, could have a Material Adverse Effect.

                  (l) No labor dispute with the employees of the Company or any
         subsidiary exists or, to the knowledge of the Company, is imminent that
         would have individually or in the aggregate a Material Adverse Effect.

                  (m) The Company and its subsidiaries own, possess or can
         acquire on reasonable terms, adequate trademarks, trade names and other
         rights to inventions, know-how, patents, copyrights, confidential
         information and other intellectual property (collectively,
         "INTELLECTUAL PROPERTY RIGHTS") necessary to conduct the business now
         operated by them, or presently employed by them, and have not received
         any notice of infringement of or conflict with asserted rights of
         others with respect to any intellectual property rights that, if
         determined adversely to the Company or any of its subsidiaries, would
         individually or in the aggregate have a Material Adverse Effect.

                  (n) Except as disclosed in the Offering Document, neither the
         Company nor any of its subsidiaries is in violation of any statute, any
         rule, regulation, decision or order of any governmental agency or body
         or any court, domestic or foreign, relating to the use, disposal or
         release of hazardous or toxic substances or relating to the protection
         or restoration of the environment or human exposure to hazardous or
         toxic substances (collectively, "ENVIRONMENTAL LAWS"), owns or operates
         any real property contaminated with any substance that is subject to
         any environmental laws, is liable for any off-site disposal or
         contamination pursuant to any environmental laws, or is subject to any
         claim relating to any environmental laws, which violation,
         contamination, liability or claim would individually or in the
         aggregate have a Material Adverse Effect; and the Company is not aware
         of any pending investigation which might lead to such a claim.

                  (o) Except as disclosed in the Offering Document, there are no
         pending actions, suits or proceedings against or affecting the Company,
         any of its subsidiaries or any of their respective properties that, if
         determined adversely to the Company or any of its subsidiaries, would
         individually or in the aggregate have a Material Adverse Effect, or
         would materially and adversely affect the ability of the Company to
         perform its obligations under the Indenture, this Agreement or the
         Registration Rights Agreement, or which are otherwise material in the
         context of the sale of the Offered Securities; and no such actions,
         suits or proceedings are threatened or, to the Company's knowledge,
         contemplated.

                  (p) The financial statements included in the Offering Document
         present fairly the financial position of the Company and its
         consolidated subsidiaries as of the dates shown and their results of
         operations and cash flows for the periods shown, and, except as
         otherwise disclosed in the Offering Document, such financial statements
         have been prepared in conformity
<PAGE>   5
                           Purchase Agreement-Page 5

         with the generally accepted accounting principles in the United States
         applied on a consistent basis.

                  (q) Except as disclosed in the Offering Document, since the
         date of the latest audited financial statements included in the
         Offering Document there has been no material adverse change, nor any
         development or event involving a prospective material adverse change,
         in the condition (financial or other), business, properties or results
         of operations of the Company and its subsidiaries taken as a whole,
         and, except as disclosed in or contemplated by the Offering Document,
         there has been no dividend or distribution of any kind declared, paid
         or made by the Company on any class of its capital stock.

                  (r) The Company is not an open-end investment company, unit
         investment trust or face-amount certificate company that is or is
         required to be registered under Section 8 of the United States
         Investment Company Act of 1940 (the "INVESTMENT COMPANY ACT"); and the
         Company is not and, after giving effect to the offering and sale of the
         Offered Securities and the application of the proceeds thereof as
         described in the Offering Document, will not be an "investment company"
         as defined in the Investment Company Act.

                  (s) No securities of the same class (within the meaning of
         Rule 144A(d)(3) under the Securities Act) as the Offered Securities are
         listed on any national securities exchange registered under Section 6
         of the Exchange Act or quoted in a U.S. automated inter-dealer
         quotation system.

                  (t) Assuming the accuracy of the representations and
         warranties in Section 4 of this Agreement, the offer and sale of the
         Offered Securities in the manner contemplated by this Agreement will be
         exempt from the registration requirements of the Securities Act by
         reason of Section 4(2) thereof or Regulation D thereunder; and it is
         not necessary to qualify an indenture in respect of the Offered
         Securities under the United States Trust Indenture Act of 1939, as
         amended (the "TRUST INDENTURE Act") in connection with the offer, sale
         and delivery of the Offered Securities to the Purchasers in the manner
         contemplated by this Agreement.

                  (u) Neither the Company, nor any of its affiliates, nor any
         person (except with respect to the Purchasers, as to whom the Company
         makes no representations or warranties) acting on its or their behalf
         (i) has, within the six-month period prior to the date hereof, offered
         or sold the Offered Securities or any security of the same class or
         series as the Offered Securities or (ii) has offered or will offer or
         sell the Offered Securities in the United States by means of any form
         of general solicitation or general advertising within the meaning of
         Rule 502(c) under the Securities Act. The Company has not entered and
         will not enter into any contractual arrangement with respect to the
         distribution of the Offered Securities except for this Agreement.

                  (v) The Company is subject to Section 13 or 15(d) of the
         Exchange Act.

                  (w) Except as disclosed in the Offering Document, there are no
         contracts, agreements or understandings between the Company and any
         person that would give rise to a valid claim against the Company or any
         Purchaser for a brokerage commission, finder's fee or other like
         payment in connection with this offering.

                  (x) Except as disclosed in the Offering Document or listed on
         Schedule 2(x) attached hereto, there are no contracts, agreements or
         understandings between the Company and any
<PAGE>   6
                           Purchase Agreement-Page 6

         person granting such person the right to require the Company to file a
         registration statement under the Securities Act with respect to any
         securities of the Company owned or to be owned by such person or to
         require the Company to include such securities in the securities
         registered pursuant to a registration statement or in any securities
         being registered pursuant to any other registration statement filed by
         the Company under the Securities Act.

                  (y) Except where the failure to file would not have a Material
         Adverse Effect, the Company and its subsidiaries have filed all
         Federal, State, local and foreign income tax returns which have been
         required to be filed and have paid all taxes indicated by said returns
         and all assessments received by them or any of them to the extent that
         such taxes have become due and are not being contested in good faith.
         All tax liabilities have been adequately provided for in the financial
         statements of the Company.

                  (z) The Company and its subsidiaries maintain a system of
         internal accounting controls sufficient to provide reasonable
         assurances that (i) transactions are executed in accordance with
         management's general or specific authorization; (ii) transactions are
         recorded as necessary to permit preparation of financial statements in
         conformity with generally accepted accounting principles and to
         maintain accountability for assets; (iii) access to assets is permitted
         only in accordance with management's general or specific authorization;
         and (iv) the recorded accountability for assets is compared with
         existing assets at reasonable intervals and appropriate action is taken
         with respect to any differences.

                  (aa) The Company and its subsidiaries carry, or are covered
         by, insurance in such amounts and covering such risks as is adequate
         for the conduct of their respective businesses and the value of their
         respective properties and as is customary for companies engaged in
         similar industries.

         3. Purchase, Sale and Delivery of Offered Securities. On the basis of
the representations, warranties and agreements herein contained, but subject to
the terms and conditions herein set forth, the Company agrees to sell to the
Purchasers, and the Purchasers agree, severally and not jointly, to purchase
from the Company, at a purchase price of 97% of the principal amount thereof,
the respective principal amounts of Firm Securities set forth opposite the names
of the several Purchasers in Schedule A hereto.

         The Company will deliver against payment of the purchase price the Firm
Securities in the form of one or more permanent global Securities in definitive
form (the "FIRM GLOBAL SECURITIES") deposited with the Trustee as custodian for
The Depository Trust Company ("DTC") and registered in the name of Cede & Co.,
as nominee for DTC. Interests in any permanent global Securities will be held
only in book-entry form through DTC, except in the limited circumstances
described in the Offering Document. Payment for the Firm Securities shall be
made by the Purchasers in Federal (same day) funds by official check or checks
or wire transfer to an account at a bank acceptable to CSFBC drawn to the order
of the Company at the office of Testa, Hurwitz & Thibeault, LLP ("TESTA
HURWITZ"), 125 High Street, Boston, MA 02110, at 9:30 A.M. (New York time), on
May 23, 2001, or at such other time not later than seven full business days
thereafter as CSFBC and the Company determine, such time being herein referred
to as the "FIRST CLOSING DATE", against delivery to the Trustee as custodian for
DTC of the Firm Global Securities representing all of the Firm Securities. The
Firm Global Securities will be made available for checking at the above office
of Testa Hurwitz at least 24 hours prior to the First Closing Date.

         In addition, upon written notice from CSFBC given to the Company from
time to time not more than 30 days subsequent to the date of this Agreement, the
Purchasers may purchase all or less than all of
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                           Purchase Agreement-Page 7


the Optional Securities at the purchase price per principal amount of Offered
Securities (including any accrued interest thereon to the related Optional
Closing Date). The Company agrees to sell to the Purchasers the number of
Optional Securities specified in such notice and the Purchasers agree, severally
and not jointly, to purchase such Optional Securities. Such Optional Securities
shall be purchased from the Company for the account of each Purchaser in the
same proportion as the number of Firm Securities set forth opposite such
Purchaser's name in Schedule A hereto bears to the total number of Firm
Securities (subject to adjustment by CSFBC to eliminate fractions) and may be
purchased by the Purchasers only for the purpose of covering over-allotments
made in connection with the sale of the Firm Securities. No Optional Securities
shall be sold or delivered unless the Firm Securities previously have been, or
simultaneously are, sold and delivered. The right to purchase the Optional
Securities or any portion thereof may be exercised from time to time and to the
extent not previously exercised may be surrendered and terminated at any time
upon notice by CSFBC to the Company.

         Each time for the delivery of and payment for the Optional Securities,
being herein referred to as the "OPTIONAL CLOSING DATE", which may be the First
Closing Date (the First Closing Date and each Optional Closing Date, if any,
being sometimes referred to as a "CLOSING DATE"), shall be determined by CSFBC
on behalf of the several Purchasers but shall not be later than seven full
business days after written notice of election to purchase Optional Securities
is given. The Company will deliver against payment of the purchase price the
Optional Securities being purchased on each Optional Closing Date in the form of
one or more permanent global Securities in definitive form (each, an "OPTIONAL
GLOBAL SECURITY") deposited with the Trustee as custodian for DTC and registered
in the name of Cede & Co., as nominee for DTC. Payment for such Optional
Securities shall be made by the Purchasers in Federal (same day) funds by
official check or checks or wire transfer to an account at a bank acceptable to
CSFBC drawn to the order of the Company at the office of Testa Hurwitz, against
delivery to the Trustee as custodian for DTC of the Optional Global Securities
representing all of the Optional Securities being purchased on such Optional
Closing Date.

         4. Representations by Purchasers; Resale by Purchasers.

                  (a) Each Purchaser severally represents and warrants to the
         Company that it is an "accredited investor" within the meaning of
         Regulation D under the Securities Act.

                  (b) Each Purchaser severally acknowledges that the Offered
         Securities have not been registered under the Securities Act and may
         not be offered or sold within the United States except pursuant to an
         exemption from, or in a transaction not subject to, the registration
         requirements of the Securities Act. Each Purchaser severally represents
         and agrees that it has not offered and sold, and will not offer or
         sell, any Offered Securities, except to qualified institutional buyers
         within the meaning of Rule 144A under the Securities Act ("RULE 144A").

                  (c) Each Purchaser severally agrees that it and each of its
         affiliates has not entered and will not enter into any contractual
         arrangement with respect to the distribution of the Offered Securities
         except for any such arrangements with the other Purchasers or
         affiliates of the other Purchasers or with the prior written consent of
         the Company.

                  (d) Each Purchaser severally agrees that it and each of its
         affiliates has not and will not offer or sell the Offered Securities in
         the United States by means of any form of general solicitation or
         general advertising within the meaning of Rule 502(c) under the
         Securities Act, including, but not limited to (i) any advertisement,
         article, notice or other communication published in any newspaper,
         magazine or similar media or broadcast over television or radio, or
<PAGE>   8
                           Purchase Agreement-Page 8


         (ii) any seminar or meeting whose attendees have been invited by any
         general solicitation or general advertising. Each Purchaser severally
         agrees, with respect to resales made in reliance on Rule 144A of any of
         the Offered Securities, to deliver either with the confirmation of such
         resale or otherwise prior to settlement of such resale a notice to the
         effect that the resale of such Offered Securities has been made in
         reliance upon the exemption from the registration requirements of the
         Securities Act provided by Rule 144A.

         5. Certain Agreements of the Company. The Company agrees with the
several Purchasers that:

                  (a) The Company will advise CSFBC promptly of any proposal to
         amend or supplement the Offering Document and will not effect such
         amendment or supplementation without CSFBC's consent. If, at any time
         prior to the completion of the resale of the Offered Securities by the
         Purchasers, any event occurs as a result of which the Offering Document
         as then amended or supplemented would include an untrue statement of a
         material fact or omit to state any material fact necessary in order to
         make the statements therein, in the light of the circumstances under
         which they were made, not misleading, or if it is necessary at any such
         time to amend or supplement the Offering Document to comply with any
         applicable law, the Company promptly will notify CSFBC of such event
         and promptly will prepare, at its own expense, an amendment or
         supplement which will correct such statement or omission or effect such
         compliance. Neither CSFBC's consent to, nor the Purchasers' delivery to
         offerees or investors of, any such amendment or supplement shall
         constitute a waiver of any of the conditions set forth in Section 6.

                  (b) The Company will furnish to CSFBC copies of any
         Preliminary Offering Circular, the Offering Document and all amendments
         and supplements to such documents, in each case as soon as available
         and in such quantities as CSFBC requests, and the Company will furnish
         to CSFBC on the date hereof three copies of the Offering Document
         signed by a duly authorized officer of the Company, one of which will
         include the independent accountants' reports therein manually signed by
         such independent accountants. At any time when the Company is not
         subject to Section 13 or 15(d) of the Exchange Act, the Company will
         promptly furnish or cause to be furnished to CSFBC (and, upon request,
         to each of the other Purchasers) and, upon request of holders and
         prospective purchasers of the Offered Securities, to such holders and
         purchasers, copies of the information required to be delivered to
         holders and prospective purchasers of the Offered Securities pursuant
         to Rule 144A(d)(4) under the Securities Act (or any successor provision
         thereto) in order to permit compliance with Rule 144A in connection
         with resales by such holders of the Offered Securities The Company will
         pay the expenses of printing and distributing to the Purchasers all
         such documents.

                  (c) The Company will arrange for the qualification of the
         Offered Securities for sale and the determination of their eligibility
         for investment under the laws of such jurisdictions in the United
         States and Canada as CSFBC designates and will continue such
         qualifications in effect so long as required for the resale of the
         Offered Securities by the Purchasers, provided that the Company will
         not be required to qualify as a foreign corporation or to file a
         general consent to service of process in any such state.

                  (d) During the period of five years hereafter, the Company
         will furnish to CSFBC and, upon request, to each of the other
         Purchasers, as soon as practicable after the end of each fiscal year, a
         copy of its annual report to stockholders for such year; and the
         Company will furnish to CSFBC and, upon request, to each of the other
         Purchasers (i) as soon as available, a copy of each
<PAGE>   9
                           Purchase Agreement-Page 9


         report and any definitive proxy statement of the Company filed with the
         Commission under the Exchange Act or mailed to stockholders, and (ii)
         from time to time, such other information concerning the Company as
         CSFBC may reasonably request.

                  (e) During the period of two years after the later of the
         First Closing Date and the last Optional Closing Date, the Company
         will, upon request, furnish to CSFBC, each of the other Purchasers and
         any holder of Offered Securities a copy of the restrictions on transfer
         applicable to the Offered Securities.

                  (f) During the period of two years after the later of the
         First Closing Date and the last Optional Closing Date, the Company will
         not, and will not permit any of its affiliates (as defined in Rule 144
         under the Securities Act) to, resell any of the Offered Securities that
         have been reacquired by any of them.

                  (g) During the period of two years after the later of the
         First Closing Date and the last Optional Closing Date, the Company will
         not be or become, an open-end investment company, unit investment trust
         or face-amount certificate company that is or is required to be
         registered under Section 8 of the Investment Company Act.

                  (h) The Company will pay all expenses incidental to the
         performance of its obligations under this Agreement, the Indenture and
         the Registration Rights Agreement, including (i) the fees and expenses
         of the Trustee and its professional advisers; (ii) all expenses in
         connection with the execution, issue, authentication, packaging and
         initial delivery of the Offered Securities , the preparation of this
         Agreement, the Registration Rights Agreement, the Offered Securities,
         the Indenture, the Offering Document and amendments and supplements
         thereto, and any other document relating to the issuance, offer, sale
         and delivery of the Offered Securities; (iii) the cost of listing the
         Offered Securities and qualifying the Offered Securities for trading in
         The Portal(SM) Market and any expenses incidental thereto; (iv) the
         cost of any advertising approved by the Company in connection with the
         issue of the Offered Securities; (v) for any expenses (including fees
         and disbursements of counsel) incurred in connection with qualification
         of the Offered Securities for sale under the laws of such jurisdictions
         in the United States and Canada as CSFBC designates and the printing of
         memoranda relating thereto and (vi) for expenses incurred in
         distributing Preliminary Offering Circulars and the Offering Document
         (including any amendments and supplements thereto) to the Purchasers.
         The Company, on the one hand, and the Purchasers, on the other hand,
         shall equally share the expenses relating to the private jet used by
         certain of the Company's officers and employees and representatives of
         the Purchasers in connection with attending meetings with prospective
         purchasers of the Offered Securities.

                  (i) In connection with the offering, until CSFBC shall have
         notified the Company and the other Purchasers of the completion of the
         resale of the Offered Securities, neither the Company nor any of its
         affiliates has or will, either alone or with one or more other persons,
         bid for or purchase for any account in which it or any of its
         affiliates has a beneficial interest any Offered Securities or attempt
         to induce any person to purchase any Offered Securities; and neither it
         nor any of its affiliates will make bids or purchases for the purpose
         of creating actual, or apparent, active trading in, or of raising the
         price of, the Offered Securities.

                  (j) The Company will not at any time offer, sell, contract to
         sell, pledge or otherwise dispose of, directly or indirectly, any
         securities under circumstances where such offer, sale,
<PAGE>   10
                           Purchase Agreement-Page 10


         pledge, contract or disposition would cause the exemption afforded by
         Section 4(2) of the Securities Act to cease to be applicable to the
         offer and sale of the Offered Securities.

                  (k) For a period of 90 days after the date of the initial
         offering of the Offered Securities by the Purchasers, the Company will
         not offer, sell, contract to sell, pledge or otherwise dispose of,
         directly or indirectly, or file with the Commission a registration
         statement under the Securities Act relating to, any shares of the
         Company's common stock, par value $.01 per share (the "COMMON STOCK"),
         or securities convertible into or exchangeable or exercisable for any
         shares of its Common Stock, or publicly disclose the intention to make
         any such offer, sale, pledge, disposition or filing, without the prior
         written consent of CSFBC, except (i) issuances of Common Stock pursuant
         to the terms of an employee stock purchase plan in effect on the date
         hereof and filing with the Commission registration statements on Form
         S-8 with respect to such employee stock purchase plan, (ii) grants of
         employee stock options pursuant to the terms of a plan in effect on the
         date hereof, issuances of Common Stock pursuant to the exercise of such
         options and filing with the Commission registration statements on Form
         S-8 with respect to such employee stock option plan, (iii) the exercise
         of any other employee stock option outstanding on the date hereof or
         (iv) except as otherwise contemplated by the Registration Rights
         Agreement.

                  (l) The Company will cause to be delivered to the Purchasers
         an agreement in substantially the form attached hereto on Schedule C
         dated on or before the date of this Agreement from the Company's
         directors and executive officers to the effect that such person or
         entity (A)(i) offer, pledge, sell, contract to sell, sell any option or
         contract to purchase, purchase any option or contract to sell, grant
         any option, right or warrant to purchase, lend, or otherwise transfer
         or dispose of, directly or indirectly, any shares of Common Stock or
         any securities convertible into or exercisable or exchangeable for
         Common Stock or (A)(ii) enter into any swap or other arrangement that
         transfers to another, in whole or in part, any of the economic
         consequences of ownership of the Common Stock, whether any such
         transaction described in clause (A)(i) or (A)(ii) above is to be
         settled by delivery of Common Stock or such other securities, in cash
         or otherwise, (B) publicly disclose the intention to effect any such
         transaction or (C) make any demand for or exercise any right with
         respect to, the registration of any shares of Common Stock or any
         security convertible into or exercisable or exchangeable for Common
         Stock, in each case, for a period of 90 days after the date hereof
         without the prior written consent of CSFBC (collectively, the "LOCKUP
         AGREEMENTS").

                  (m) In connection with the sale of the Offered Securities to
         the Purchasers, the Company will file the notice on Form D required by
         Rule 503 under the Securities Act within the time required by such Rule
         and otherwise in compliance with such Rule. A copy of such notice shall
         be furnished promptly to CSFBC.

         6. Conditions of the Obligations of the Purchasers. The obligations of
the several Purchasers to purchase and pay for the Firm Securities on the First
Closing Date and for the Optional Securities on each Optional Closing Date will
be subject to the accuracy of the representations and warranties on the part of
the Company herein, to the accuracy of the statements of officers of the Company
made pursuant to the provisions hereof, to the performance by the Company of its
obligations hereunder and to the following additional conditions precedent:

                  (a) The Purchasers shall have received a letter, dated the
         date of this Agreement, of PricewaterhouseCoopers LLP confirming that
         they are independent public accountants within the
<PAGE>   11
                           Purchase Agreement-Page 11

         meaning of the Securities Act and the applicable published rules and
         regulations thereunder ("RULES AND REGULATIONS") and to the effect
         that:

                           (i) in their opinion the financial statements
                  examined by them and included in the Offering Document and in
                  the Exchange Act Reports comply as to form in all material
                  respects with the applicable accounting requirements of the
                  Securities Act and the related published Rules and
                  Regulations;

                           (ii) they have performed the procedures specified by
                  the American Institute of Certified Public Accountants for a
                  review of interim financial information as described in
                  Statement of Auditing Standards No. 71, Interim Financial
                  Information, on the unaudited financial statements included in
                  the Offering Document and in the Exchange Act Reports;

                           (iii) on the basis of the review referred to in
                  clause (ii) above, a reading of the latest available interim
                  financial statements of the Company, inquiries of officials of
                  the Company who have responsibility for financial and
                  accounting matters and other specified procedures, nothing
                  came to their attention that caused them to believe that:

                                    (A) the unaudited financial statements and
                           summary of earnings included in the Offering Document
                           do not comply as to form in all material respects
                           with the applicable accounting requirements of the
                           Securities Act and the related published Rules and
                           Regulations or any material modifications should be
                           made to such unaudited financial statements for them
                           to be in conformity with generally accepted
                           accounting principles;

                                    (B) at the date of the latest available
                           balance sheet read by such accountants, or at a
                           subsequent specified date not more than three
                           business days prior to the date of this Agreement,
                           there was any change in the capital stock or any
                           increase in short-term indebtedness or long-term debt
                           of the Company and its consolidated subsidiaries or,
                           at the date of the latest available balance sheet
                           read by such accountants, there was any decrease in
                           consolidated net current assets or net assets, as
                           compared with amounts shown on the latest balance
                           sheet included in the Offering Document and the
                           Exchange Act Reports; or

                                    (C) for the period from the closing date of
                           the latest income statement included in the Offering
                           Document and the Exchange Act Reports to the closing
                           date of the latest available income statement read by
                           such accountants there were any decreases, as
                           compared with the corresponding period of the
                           previous year and with the period of corresponding
                           length ended the date of the latest income statement
                           included in the Offering Document, in consolidated
                           net sales, net operating income or in the total or
                           per share amounts of consolidated net income or in
                           the ratio of earnings to fixed charges;

                  except in all cases set forth in clauses (A), (B) and (C)
                  above for changes, increases or decreases which the Offering
                  Document disclose have occurred or may occur or which are
                  described in such letter; and
<PAGE>   12
                           Purchase Agreement-Page 12


                           (iv) they have compared specified dollar amounts (or
                  percentages derived from such dollar amounts) and other
                  financial information contained in the Offering Document and
                  the Exchange Act Reports (in each case to the extent that such
                  dollar amounts, percentages and other financial information
                  are derived from the general accounting records of the Company
                  and its subsidiaries subject to the internal controls of the
                  Company's accounting system or are derived directly from such
                  records by analysis or computation) with the results obtained
                  from inquiries, a reading of such general accounting records
                  and other procedures specified in such letter and have found
                  such dollar amounts, percentages and other financial
                  information to be in agreement with such results, except as
                  otherwise specified in such letter.

                  (b) Subsequent to the execution and delivery of this
         Agreement, there shall not have occurred (i) a change in U.S. or
         international financial, political or economic conditions or currency
         exchange rates or exchange controls as would, in the judgment of CSFBC,
         be likely to prejudice materially the success of the proposed issue,
         sale or distribution of the Offered Securities, whether in the primary
         market or in respect of dealings in the secondary market, or (ii) (A)
         any change, or any development or event involving a prospective change,
         in the condition (financial or other), business, properties or results
         of operations of the Company or its subsidiaries taken as a whole
         which, in the judgment of a majority in interest of the Purchasers
         including CSFBC, is material and adverse and makes it impractical or
         inadvisable to proceed with completion of the offering or the sale of
         and payment for the Offered Securities; (B) any downgrading in the
         rating of any debt securities of the Company by any "nationally
         recognized statistical rating organization" (as defined for purposes of
         Rule 436(g) under the Securities Act), or any public announcement that
         any such organization has under surveillance or review its rating of
         any debt securities of the Company (other than an announcement with
         positive implications of a possible upgrading, and no implication of a
         possible downgrading, of such rating); (C) any material suspension or
         material limitation of trading in securities generally on The Nasdaq
         National Market or The New York Stock Exchange, or any setting of
         minimum prices for trading on such exchange, or any suspension of
         trading of any securities of the Company on any exchange or in the
         over-the-counter market; (D) any banking moratorium declared by U.S.
         Federal or New York authorities; or (E) any outbreak or escalation of
         major hostilities in which the United States is involved, any
         declaration of war by Congress or any other substantial national or
         international calamity or emergency if, in the judgment of a majority
         in interest of the Purchasers including CSFBC, the effect of any such
         outbreak, escalation, declaration, calamity or emergency makes it
         impractical or inadvisable to proceed with completion of the offering
         or sale of and payment for the Offered Securities.

                  (c) (1) The Purchasers shall have received an opinion, dated
         such Closing Date, of Brown, Rudnick, Freed & Gesmer, P.C., counsel for
         the Company, to the effect that:


                           (i) The Company has been duly incorporated and is an
                  existing corporation in good standing under the laws of the
                  State of Delaware, with corporate power and authority to own
                  its properties and conduct its business as described in the
                  Offering Document; and the Company is duly qualified to do
                  business as a foreign corporation in good standing in
                  Massachusetts and California;

                           (ii) Brooks Automation Massachusetts Securities
                  Corporation has been duly incorporated and is an existing
                  corporation in good standing under the laws of the
<PAGE>   13
                           Purchase Agreement-Page 13


                  Commonwealth of Massachusetts, with corporate power and
                  authority to own its properties and conduct its business as
                  described in the Offering Document; and all of its issued and
                  outstanding shares have been duly and validly authorized and
                  issued, are fully paid and nonassessable and, unless otherwise
                  stated in the Offering Document, are owned of record by the
                  Company directly, to such counsel's knowledge, free and clear
                  of all liens, encumbrances, equities, claims, security
                  interests, voting trusts or other defects of title whatsoever;

                           (iii) The Indenture has been duly authorized,
                  executed and delivered; the Offered Securities delivered on
                  such Closing Date have been duly authorized, executed,
                  authenticated, issued and delivered and conform to the
                  description thereof contained in the Offering Document; and
                  the Indenture and the Offered Securities delivered on such
                  Closing Date constitute valid and legally binding obligations
                  of the Company enforceable in accordance with their terms,
                  subject to bankruptcy, insolvency, fraudulent transfer,
                  reorganization, moratorium and similar laws of general
                  applicability relating to or affecting creditors' rights and
                  to general equity principles;

                           (iv) The Offered Securities delivered on such Closing
                  Date are convertible into Common Stock of the Company in
                  accordance with the terms of the Indenture; the shares of such
                  Common Stock initially issuable upon conversion of the Offered
                  Securities delivered on such Closing Date have been duly
                  authorized and reserved for issuance upon such conversion and,
                  when issued upon such conversion in accordance with the terms
                  of the Indenture, will be validly issued, fully paid and
                  nonassessable; the outstanding shares of such Common Stock
                  have been duly authorized and validly issued, are fully paid
                  and nonassessable and conform to the description thereof
                  contained in the Offering Document; and the stockholders of
                  the Company have no preemptive rights with respect to the
                  Offered Securities or the Underlying Shares under the
                  Company's Certificate of Incorporation, under Delaware General
                  Corporation Law or, to such counsel's knowledge, otherwise;

                           (v) No consent, approval, authorization or order of,
                  or filing with, any governmental agency or body or any court
                  is required for the consummation of the transactions
                  contemplated by this Agreement and the Registration Rights
                  Agreement in connection with the issuance or sale of the
                  Offered Securities by the Company, except such as may be
                  required under state securities laws and except for the order
                  of the Commission declaring the Shelf Registration Statement
                  effective and except for the filing of a notice of sale on
                  Form D as required by Rule 503 of Regulation D of the
                  Securities Act;

                           (vi) To such counsel's knowledge, there are no
                  pending actions, suits or proceedings against or affecting the
                  Company, any of its subsidiaries or any of their respective
                  properties that, if determined adversely to the Company or any
                  of its subsidiaries, would materially and adversely affect the
                  ability of the Company to perform its obligations under the
                  Indenture, this Agreement or the Registration Rights
                  Agreement; and such counsel do not know of any legal or
                  governmental proceedings that would be required to be
                  disclosed by the Company under Item 103 under Regulation S-K
                  promulgated under the Securities Act;
<PAGE>   14
                           Purchase Agreement-Page 14


                           (vii) The execution, delivery and performance of the
                  Indenture, this Agreement and the Registration Rights
                  Agreement and the issuance and sale of the Offered Securities
                  and Underlying Shares will not result in a breach or violation
                  of any of the terms and provisions of, or constitute a default
                  under, any statute, any rule, regulation or order of any
                  governmental agency or body or any court having jurisdiction
                  over the Company or any Material Subsidiary (which, for
                  purposes of this (vii) only, shall include Brooks Automation
                  Japan (KK)) of the Company or any of their properties
                  (provided, however, that with respect to such opinion given
                  with respect to any Material Subsidiary which is not organized
                  or incorporated within the United States, such opinion is
                  given to such counsel's knowledge), or, to such counsel's
                  knowledge, any agreement or instrument to which the Company or
                  any Material Subsidiary is a party or by which the Company or
                  any Material Subsidiary is bound or to which any of the
                  properties of the Company or any Material Subsidiary is
                  subject, or the charter or by-laws of the Company or any
                  Material Subsidiary organized or incorporated within the
                  United States, and the Company has full power and authority to
                  authorize, issue and sell the Offered Securities and
                  Underlying Shares as contemplated by this Agreement;

                           (viii) Such counsel has participated in conferences
                  with officers and other representatives of the Company, and
                  representatives of the independent public accountants for the
                  Company, and your representatives, at which conferences the
                  contents of the Offering Document and related matters were
                  discussed and, although such counsel need not pass upon, nor
                  assume any responsibility for, the accuracy, completeness or
                  fairness of the statements contained in the Offering Document,
                  no facts have come to the attention of such counsel that cause
                  such counsel to believe that the Offering Document, as of the
                  date hereof and of such Closing Date, contained any untrue
                  statement of a material fact or omitted to state any material
                  fact necessary to make the statements therein, in light of the
                  circumstances under which they were made, not misleading, it
                  being understood that such counsel need express no belief with
                  respect to the financial statements, the notes thereto and
                  related schedules, or other financial data or statistical data
                  derived from the financial statements included in, or omitted
                  from, the Offering Document;

                           (ix) This Agreement and the Registration Rights
                  Agreement have each been duly authorized, executed and
                  delivered by the Company;

                           (x) It is not necessary in connection with (i) the
                  offer, sale and delivery of the Offered Securities by the
                  Company to the several Purchasers pursuant to this Agreement
                  or (ii) the resales of the Offered Securities by the several
                  Purchasers in the manner contemplated by this Agreement, to
                  register the Offered Securities or Offered Stock under the
                  Securities Act or to qualify an indenture in respect thereof
                  under the Trust Indenture Act; and

                           (xi) The Company is not and, after giving effect to
                  the offering and sale of the Offered Securities and the
                  application of the proceeds thereof as described in the
                  Offering Document, will not be an "investment company" as
                  defined in the Investment Company Act.

                  (2) The Purchasers shall have received an opinion, dated such
              Closing Date, from each of the following: local counsel in Germany
              for Brooks Automation GmbH and Brooks
<PAGE>   15
                           Purchase Agreement-Page 15


              Automation Holding GmbH and local counsel in Japan for Brooks
              Automation Japan (KK); in each case to the effect that each such
              company has been duly incorporated and is an existing corporation
              in good standing under the laws of the jurisdiction of its
              incorporation or organization, with corporate power and authority
              to own its properties and conduct its business as described in the
              Offering Document, that, if applicable, each such company is duly
              qualified to do business as a foreign corporation in good standing
              in all other jurisdictions in which its ownership or lease of
              property or the conduct of its business requires such
              qualification and that all of the issued and outstanding shares or
              equivalent equity interests of each such company have been duly
              and validly authorized and issued, are fully paid and
              nonassessable and, unless otherwise stated in the Offering
              Document, are owned of record by the Company, directly or
              indirectly through another subsidiary, to such counsel's knowledge
              free and clear of all liens, encumbrances, equities, claims,
              security interests, voting trusts or other defects of title
              whatsoever.

                  (3) The Purchasers shall have received an opinion, dated such
              Closing Date, of Perman & Green, patent counsel for the Company,
              in form and substance reasonably satisfactory in all respects to
              the Purchasers and their counsel.

                  (d) The Purchasers shall have received from Testa Hurwitz,
         counsel for the Purchasers, such opinion or opinions, dated such
         Closing Date, with respect to the incorporation of the Company, the
         validity of the Offered Securities delivered on such Closing Date, the
         Offering Circular, the exemption from registration for the offer and
         sale of the Offered Securities by the Company to the several Purchasers
         and the resales by the several Purchasers as contemplated hereby and
         other related matters as CSFBC may require, and the Company shall have
         furnished to such counsel such documents as they request for the
         purpose of enabling them to pass upon such matters.

                  (e) The Purchasers shall have received a certificate, dated
         such Closing Date, of the President or any Vice President and a
         principal financial or accounting officer of the Company in which such
         officers, to the best of their knowledge after reasonable
         investigation, shall state that the representations and warranties of
         the Company in this Agreement are true and correct, that the Company
         has complied with all agreements and satisfied all conditions on its
         part to be performed or satisfied hereunder at or prior to such Closing
         Date, and that, subsequent to the respective dates of the most recent
         financial statements in the Offering Document there has been no
         material adverse change, nor any development or event involving a
         prospective material adverse change, in the condition (financial or
         other), business, properties or results of operations of the Company
         and its subsidiaries taken as a whole except as set forth in or
         contemplated by the Offering Document or as described in such
         certificate.

                  (f) The Purchasers shall have received a letter, dated such
         Closing Date, of PricewaterhouseCoopers LLP which meets the
         requirements of subsection (a) of this Section, except that the
         specified date referred to in such subsection will be a date not more
         than three days prior to such Closing Date for the purposes of this
         subsection.

                  (g) On or prior to the date of this Agreement, the Purchasers
         shall have received Lockup Letters from each of the executive officers
         and directors of the Company.
<PAGE>   16
                           Purchase Agreement-Page 16


         Documents described as being "in the agreed form" are documents which
are in the forms which have been initialed for the purpose of identification by
Testa, Hurwitz & Thibeault, LLP, copies of which are held by the Company and
CSFBC, with such changes as CSFBC may approve.

         The Company will furnish the Purchasers with such conformed copies of
such opinions, certificates, letters and documents as the Purchasers reasonably
request. CSFBC may in its sole discretion waive on behalf of the Purchasers
compliance with any conditions to the obligations of the Purchasers hereunder,
whether in respect of an Optional Closing Date or otherwise.

         7. Indemnification and Contribution. (a) The Company will indemnify and
hold harmless each Purchaser, its partners, directors and officers and each
person, if any, who controls such Purchaser within the meaning of Section 15 of
the Securities Act, against any losses, claims, damages or liabilities, joint or
several, to which such Purchaser may become subject, under the Securities Act or
the Exchange Act or otherwise, insofar as such losses, claims, damages or
liabilities (or actions in respect thereof) arise out of or are based upon any
untrue statement or alleged untrue statement of any material fact contained in
the Offering Document, or any amendment or supplement thereto, or any related
preliminary offering circular or the Exchange Act Reports, or arise out of or
are based upon the omission or alleged omission to state therein a material fact
necessary in order to make the statements therein, in the light of the
circumstances under which they were made, not misleading, including any losses,
claims, damages or liabilities arising out of or based upon the Company's
failure to perform its obligations under Section 5(a) of this Agreement, and
will reimburse each Purchaser for any legal or other expenses reasonably
incurred by such Purchaser in connection with investigating or defending any
such loss, claim, damage, liability or action as such expenses are incurred;
provided, however, that the Company will not be liable in any such case to the
extent that any such loss, claim, damage or liability arises out of or is based
upon an untrue statement or alleged untrue statement in or omission or alleged
omission from any of such documents in reliance upon and in conformity with
written information furnished to the Company by any Purchaser through CSFBC
specifically for use therein, it being understood and agreed that the only such
information consists of the information described as such in subsection (b)
below; and provided, further, that with respect to any untrue statement or
alleged untrue statement in or omission or alleged omission from any Preliminary
Offering Circular, the indemnity agreement contained in this subsection (a)
shall not inure to the benefit of any Purchaser that sold the Offered Securities
concerned to the person asserting any such losses, claims, damages or
liabilities, to the extent that such sale was an initial resale by such
Purchaser and any such loss, claim, damage or liability of such Purchaser
results from the fact that there was not sent or given to such person, at or
prior to the written confirmation of the sale of such Offered Securities to such
person, a copy of the Offering Document (exclusive of any material included
therein but not attached thereto) if the Company had previously furnished copies
thereof to such Purchaser.

              (b) Each Purchaser will severally and not jointly indemnify and
hold harmless the Company, its directors and officers and each person, if any,
who controls the Company within the meaning of Section 15 of the Securities Act,
against any losses, claims, damages or liabilities to which the Company may
become subject, under the Securities Act or the Exchange Act or otherwise,
insofar as such losses, claims, damages or liabilities (or actions in respect
thereof) arise out of or are based upon any untrue statement or alleged untrue
statement of any material fact contained in the Offering Document, or any
amendment or supplement thereto, or any related preliminary offering circular,
or arise out of or are based upon the omission or the alleged omission to state
therein a material fact necessary in order to make the statements therein, in
the light of the circumstances under which they were made, not misleading, in
each case to the extent, but only to the extent, that such untrue statement or
alleged untrue statement or omission or alleged omission was made in reliance
upon and in conformity with written information furnished to the Company by such
Purchaser through CSFBC specifically for
<PAGE>   17
                           Purchase Agreement-Page 17


use therein, and will reimburse any legal or other expenses reasonably incurred
by the Company in connection with investigating or defending any such loss,
claim, damage, liability or action as such expenses are incurred, it being
understood and agreed that the only such information furnished by any Purchaser
consists of the following information in the Offering Document: under the
caption "Plan of Distribution", the ninth paragraph (stating there is no market
with respect to the securities, etc.) and the eleventh paragraph (describing
certain activities of the initial purchasers, etc.); provided, however, that the
Purchasers shall not be liable for any losses, claims, damages or liabilities
arising out of or based upon the Company's failure to perform its obligations
under Section 5(a) of this Agreement.

              (c) Promptly after receipt by an indemnified party under this
Section of notice of the commencement of any action, such indemnified party
will, if a claim in respect thereof is to be made against the indemnifying party
under subsection (a) or (b) above, notify the indemnifying party of the
commencement thereof; but the omission so to notify the indemnifying party will
not relieve it from any liability which it may have to any indemnified party
otherwise than under subsection (a) or (b) above. In case any such action is
brought against any indemnified party and it notifies the indemnifying party of
the commencement thereof, the indemnifying party will be entitled to participate
therein and, to the extent that it may wish, jointly with any other indemnifying
party similarly notified, to assume the defense thereof, with counsel
satisfactory to such indemnified party (who shall not, except with the consent
of the indemnified party, be counsel to the indemnifying party), and after
notice from the indemnifying party to such indemnified party of its election so
to assume the defense thereof, the indemnifying party will not be liable to such
indemnified party under this Section for any legal or other expenses
subsequently incurred by such indemnified party in connection with the defense
thereof other than reasonable costs of investigation. No indemnifying party
shall, without the prior written consent of the indemnified party, effect any
settlement of any pending or threatened action in respect of which any
indemnified party is or could reasonably be expected to have been a party and
indemnity could have been sought hereunder by such indemnified party unless such
settlement includes an unconditional release of such indemnified party from all
liability on any claims that are the subject matter of such action and does not
include a statement as to or an admission of fault, culpability or failure to
act by or on behalf of any indemnified party. No indemnified party shall effect
any settlement of any pending or threatened action without the prior written
consent of the indemnifying party, which such consent shall not be unreasonably
withheld or delayed.

              (d) If the indemnification provided for in this Section is
unavailable or insufficient to hold harmless an indemnified party under
subsection (a) or (b) above, then each indemnifying party shall contribute to
the amount paid or payable by such indemnified party as a result of the losses,
claims, damages or liabilities referred to in subsection (a) or (b) above (i) in
such proportion as is appropriate to reflect the relative benefits received by
the Company on the one hand and the Purchasers on the other from the offering of
the Offered Securities or (ii) if the allocation provided by clause (i) above is
not permitted by applicable law, in such proportion as is appropriate to reflect
not only the relative benefits referred to in clause (i) above but also the
relative fault of the Company on the one hand and the Purchasers on the other in
connection with the statements or omissions which resulted in such losses,
claims, damages or liabilities as well as any other relevant equitable
considerations. The relative benefits received by the Company on the one hand
and the Purchasers on the other shall be deemed to be in the same proportion as
the total net proceeds from the offering (before deducting expenses) received by
the Company bear to the total discounts and commissions received by the
Purchasers from the Company under this Agreement. The relative fault shall be
determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or the omission or alleged omission to state
a material fact relates to information supplied by the Company or the Purchasers
and the parties' relative intent, knowledge, access to information and
opportunity to correct or prevent such untrue
<PAGE>   18
                           Purchase Agreement-Page 18


statement or omission. The amount paid by an indemnified party as a result of
the losses, claims, damages or liabilities referred to in the first sentence of
this subsection (d) shall be deemed to include any legal or other expenses
reasonably incurred by such indemnified party in connection with investigating
or defending any action or claim which is the subject of this subsection (d).
Notwithstanding the provisions of this subsection (d), no Purchaser shall be
required to contribute any amount in excess of the amount by which the total
price at which the Offered Securities purchased by it were resold exceeds the
amount of any damages which such Purchaser has otherwise been required to pay by
reason of such untrue or alleged untrue statement or omission or alleged
omission. The Purchasers' obligations in this subsection (d) to contribute are
several in proportion to their respective purchase obligations and not joint.

              (e) The obligations of the Company under this Section shall be in
addition to any liability which the Company may otherwise have and shall extend,
upon the same terms and conditions, to each person, if any, who controls any
Purchaser within the meaning of the Securities Act or the Exchange Act; and the
obligations of the Purchasers under this Section shall be in addition to any
liability which the respective Purchasers may otherwise have and shall extend,
upon the same terms and conditions, to each person, if any, who controls the
Company within the meaning of the Securities Act or the Exchange Act.

         8. Default of Purchasers. If any Purchaser or Purchasers default in
their obligations to purchase Offered Securities hereunder on either the First
Closing Date or any Optional Closing Date and the aggregate principal amount of
Offered Securities that such defaulting Purchaser or Purchasers agreed but
failed to purchase does not exceed 10% of the total principal amount of Offered
Securities that the Purchasers are obligated to purchase on such Closing Date,
CSFBC may make arrangements satisfactory to the Company for the purchase of such
Offered Securities by other persons, including any of the Purchasers, but if no
such arrangements are made by such Closing Date, the non-defaulting Purchasers
shall be obligated severally, in proportion to their respective commitments
hereunder, to purchase the Offered Securities that such defaulting Purchasers
agreed but failed to purchase on such Closing Date. If any Purchaser or
Purchasers so default and the aggregate principal amount of Offered Securities
with respect to which such default or defaults occur exceeds 10% of the total
principal amount of Offered Securities that the Purchasers are obligated to
purchase on such Closing Date and arrangements satisfactory to CSFBC and the
Company for the purchase of such Offered Securities by other persons are not
made within 36 hours after such default, this Agreement will terminate without
liability on the part of any non-defaulting Purchaser or the Company, except as
provided in Section 9 (provided that if such default occurs with respect to
Optional Securities after the First Closing Date, this Agreement shall not
terminate as to the Firm Securities or any Optional Securities purchased prior
to such termination). As used in this Agreement, the term "Purchaser" includes
any person substituted for a Purchaser under this Section. Nothing herein will
relieve a defaulting Purchaser from liability for its default.

         9. Survival of Certain Representations and Obligations. The respective
indemnities, agreements, representations, warranties and other statements of the
Company or its officers and of the several Purchasers set forth in or made
pursuant to this Agreement will remain in full force and effect, regardless of
any investigation, or statement as to the results thereof, made by or on behalf
of any Purchaser, the Company or any of their respective representatives,
officers or directors or any controlling person, and will survive delivery of
and payment for the Offered Securities. If this Agreement is terminated pursuant
to Section 8 or if for any reason the purchase of the Offered Securities by the
Purchasers is not consummated, the Company shall remain responsible for the
expenses to be paid or reimbursed by it pursuant to Section 5 and the respective
obligations of the Company and the Purchasers pursuant to Section 7 shall remain
in effect and if any Offered Securities have been purchased hereunder
<PAGE>   19
                           Purchase Agreement-Page 19


the representations and warranties in Section 2 and all obligations under
Section 5 shall also remain in effect. If the purchase of the Offered Securities
by the Purchasers is not consummated for any reason other than solely because of
the termination of this Agreement pursuant to Section 8 or the occurrence of any
event specified in clause (C), (D) or (E) of Section 6(b)(ii), the Company will
reimburse the Purchasers for all out-of-pocket expenses (including fees and
disbursements of counsel) reasonably incurred by them in connection with the
offering of the Offered Securities.

         10. Notices. All communications hereunder will be in writing and, if
sent to the Purchasers will be mailed, delivered or telegraphed and confirmed to
the Purchasers, c/o Credit Suisse First Boston Corporation, Eleven Madison
Avenue, New York, N.Y. 10010-3629, Attention: Investment Banking Department -
Transactions Advisory Group, or, if sent to the Company, will be mailed,
delivered or telegraphed and confirmed to it at 15 Elizabeth Drive, Chelmsford,
MA 01824, Attention: President; provided, however, that any notice to a
Purchaser pursuant to Section 7 will be mailed, delivered or telegraphed and
confirmed to such Purchaser.

         11. Successors. This Agreement will inure to the benefit of and be
binding upon the parties hereto and their respective successors and the
controlling persons referred to in Section 7, and no other person will have any
right or obligation hereunder, except that holders of Offered Securities shall
be entitled to enforce the agreements for their benefit contained in the second
and third sentences of Section 5(b) hereof against the Company as if such
holders were parties thereto.

         12. Representation of Purchasers. You will act for the several
Purchasers in connection with this purchase, and any action under this Agreement
taken by you jointly or by CSFBC will be binding upon all the Purchasers.

         13. Counterparts. This Agreement may be executed in any number of
counterparts, each of which shall be deemed to be an original, but all such
counterparts shall together constitute one and the same Agreement.

         14. Applicable Law. THIS AGREEMENT SHALL BE GOVERNED BY, AND CONSTRUED
IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO
PRINCIPLES OF CONFLICTS OF LAWS. The Company hereby submits to the non-exclusive
jurisdiction of the Federal and state courts in the Borough of Manhattan in The
City of New York in any suit or proceeding arising out of or relating to this
Agreement or the transactions contemplated hereby.


                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
                      [SIGNATURE PAGE IMMEDIATELY FOLLOWS]
<PAGE>   20
                      Signature Page to Purchase Agreement


If the foregoing is in accordance with the Purchasers' understanding of our
agreement, kindly sign and return to us one of the counterparts hereof,
whereupon it will become a binding agreement between the Company and the several
Purchasers in accordance with its terms.

                                 Very truly yours,

                                 BROOKS AUTOMATION, INC.


                                 By: /s/ Ellen B. Richstone
                                     ----------------------
                                     Ellen B. Richstone
                                     Senior Vice President, Finance and
                                     Administration and Chief Financial Officer


The foregoing Purchase Agreement
  is hereby confirmed and accepted
  as of the date first above written.

CREDIT SUISSE FIRST BOSTON CORPORATION
SG COWEN SECURITIES CORPORATION

  Acting on behalf of themselves
  and as the Representatives of
  the several Purchasers


By CREDIT SUISSE FIRST BOSTON CORPORATION


     By./s/ Kevin Tice
        --------------
     Title: Managing Director
<PAGE>   21
                                   SCHEDULE A


<TABLE>
<CAPTION>
                                                                  PRINCIPAL AMOUNT OF
            PURCHASER                                               FIRM SECURITIES
            ---------                                               ---------------
<S>                                                               <C>
Credit Suisse First Boston Corporation.......................         $105,000,000
SG Cowen Securities Corporation                                         45,000,000
                                                                      ------------
                              Total..........................         $150,000,000
                                                                      ============
</TABLE>
<PAGE>   22
                                   SCHEDULE B

                              MATERIAL SUBSIDIARIES

<TABLE>
<CAPTION>
---------------------------------------------------------------------------------------------------------------
                                                               Jurisdiction of        Jurisdictions in which
                                                               incorporation or     such entity is qualified to
Subsidiary                                                       organization            conduct business
---------------------------------------------------------------------------------------------------------------
<S>                                                            <C>                  <C>
Brooks Automation Massachusetts Securities Corporation          Massachusetts                  None
---------------------------------------------------------------------------------------------------------------
Brooks Automation GmbH                                             Germany                     None
---------------------------------------------------------------------------------------------------------------
Brooks Automation Holding GmbH                                     Germany                     None
---------------------------------------------------------------------------------------------------------------
</TABLE>
<PAGE>   23
                                 SCHEDULE 2(x)

The Company has granted registration rights to certain individuals in connection
with its acquisition of SimCon N.V. In addition, the Company expects to grant
registration rights to KLA-Tencor, Inc. in connection with the Company's
proposed acquisition of certain assets of KLA-Tencor, Inc. The Company also
expects to grant registration rights to certain individuals in connection with
the Company's proposed acquisition of CCS Technology, Inc. The Company may grant
registration rights in connection with other possible future acquisitions.
<PAGE>   24
                                   SCHEDULE C

                            FORM OF LOCKUP AGREEMENT