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                                                                    Exhibit 5.01



                                              September 25, 2001



Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, MA 01824

      Re:      Registration Statement on Form S-3 of Brooks Automation, Inc.


Ladies and Gentlemen:

         We have acted as counsel to Brooks Automation, Inc., a Delaware
corporation (the "Company"), in connection with the preparation and filing with
the Securities and Exchange Commission (the "Commission") of a Registration
Statement on Form S-3 (the "Registration Statement") pursuant to which the
Company is registering under the Securities Act of 1933, as amended (the "Act"),
a total of 715,004 shares of the Company's common stock, $.01 par value (the
"Company Shares") and 715,004 preferred share purchase rights (the "Rights").
Pursuant to the Registration Statement, certain of the Company's stockholders
(the "Selling Stockholders") propose to sell the Company Shares. The Rights
being registered pursuant to the Registration Statement represent Rights issued
in connection with each of the Company Shares. The Selling Stockholders, the
former stockholders of Progressive Technologies Inc., obtained their Company
Shares in connection with the Company's acquisition of Progressive Technologies
Inc. on July 12, 2001.

         For purposes of this opinion, we have assumed, without any
investigation, (i) the legal capacity of each natural person, (ii) the full
power and authority of each entity and person other than the Company to execute,
deliver and perform each document heretofore executed and delivered or hereafter
to be executed and delivered and to do each other act heretofore done or
hereafter to be done by such entity or person, (iii) the due authorization by
each entity or person other than the Company of each document heretofore
executed and delivered or hereafter to be executed and delivered and to do each
other act heretofore done or to be done by such entity or person, (iv) the due
execution and delivery by each entity or person other than the Company of each
document heretofore executed and delivered or hereafter to be executed and
delivered by such entity or person, (v) the legality, validity, binding effect
and enforceability of each document heretofore executed and delivered or
hereafter to be executed and delivered by each entity or person other than the
Company and of each other act heretofore done or hereafter to be done by such
entity or person, (vi) the genuineness of each signature on, and the
completeness of each document submitted to us as an original, (vii) the
conformity to the original of each document submitted to us as a copy, (viii)
the

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September 25, 2001
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authenticity of the original of each document submitted to us as a copy,
(ix) the completeness, accuracy and proper indexing of all governmental and
judicial records searched and (x) no modification of any provision of any
document, no waiver of any right or remedy and no exercise of any right or
remedy other than in a commercially reasonable and conscionable manner and in
good faith.

         In connection with this opinion, we have examined the following
(collectively, the "Documents"):

         (i)     the Certificate of Incorporation of the Company, as amended;
         (ii)    the Bylaws of the Company;
         (iii)   the corporate minute books or other records of the Company;
         (iv)    the Agreement and Plan of Merger relating to the acquisition of
                 Progressive Technologies Inc.;
         (v)     the Rights Agreement between the Company and Bank Boston, N.A.,
                 as Rights Agent dated as of July 23, 1997 (the "Rights
                 Agreement"); and
         (vi)    the Registration Statement.

         The opinions expressed herein are based solely upon (i) our review of
the Documents, (ii) discussions with those of our attorneys who have devoted
substantive attention to the matters contained herein, and (iii) such review of
published sources of law as we have deemed necessary.

         We have not, except as specifically noted herein, made any independent
review or investigation of orders, judgments, rules or other regulations or
decrees by which the Company or any of its property may be bound. Nor have we
made any independent investigation as to the existence of actions, suits,
investigations, or proceedings, if any, pending or threatened against the
Company.

         Our opinions contained herein are limited to the laws of The
Commonwealth of Massachusetts, the General Corporation Law of the State of
Delaware and the federal law of the United States of America.

         Based upon and subject to the foregoing, we are of the opinion that:
(i) the Company Shares are duly authorized, validly issued, fully paid and
non-assessable; and (ii) the Rights are duly authorized, validly issued, fully
paid and non-assessable.

         We understand that this opinion is to be used in connection with the
Registration Statement. We consent to the filing of this opinion as an exhibit
to said Registration Statement and to the


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September 25, 2001
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reference to our firm wherever it appears in the Registration Statement,
including the prospectus constituting a part thereof and any amendments and
supplements thereto.


                                      Very truly yours,

                                      BROWN, RUDNICK, FREED & GESMER
                                        By:  BROWN, RUDNICK, FREED & GESMER,
                                        P.C., a general partner

                                        By: /s/ Samuel P. Williams
                                            ------------------------------------
                                            Samuel P. Williams, a Member
SPW/DHM/RLM                                 duly authorized