Ownership Submission
FORM 4
Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
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(Print or Type Responses)
1. Name and Address of Reporting Person *
LEPOFSKY ROBERT
  2. Issuer Name and Ticker or Trading Symbol
BROOKS AUTOMATION INC [BRKS]
5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
__X__ Director _____ 10% Owner
_____ Officer (give title below) _____ Other (specify below)
(Last)
(First)
(Middle)
C/O BROOKS AUTOMATION, INC., 15 ELIZABETH DRIVE
3. Date of Earliest Transaction (Month/Day/Year)
10/26/2005
(Street)

CHELMSFORD, MA 01824
4. If Amendment, Date Original Filed(Month/Day/Year)
6. Individual or Joint/Group Filing(Check Applicable Line)
_X_ Form filed by One Reporting Person
___ Form filed by More than One Reporting Person
(City)
(State)
(Zip)
Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3)
2. Transaction Date (Month/Day/Year) 2A. Deemed Execution Date, if any (Month/Day/Year) 3. Transaction Code
(Instr. 8)
4. Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5)
5. Amount of Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 3 and 4)
6. Ownership Form: Direct (D) or Indirect (I)
(Instr. 4)
7. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V Amount (A) or (D) Price
Common Stock 10/26/2005   A   283,131 A (1) 283,131 D  
Common Stock 10/26/2005   A   2,170 A (2) 2,170 I By 401(k) Plan
Common Stock 10/26/2005   A   44,400 A (3) 44,400 I By Trust (4)

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Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned
(e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security
(Instr. 3)
2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (Month/Day/Year) 3A. Deemed Execution Date, if any (Month/Day/Year) 4. Transaction Code
(Instr. 8)
5. Number of Derivative Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4, and 5)
6. Date Exercisable and Expiration Date
(Month/Day/Year)
7. Title and Amount of Underlying Securities
(Instr. 3 and 4)
8. Price of Derivative Security
(Instr. 5)
9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 4)
10. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 4)
11. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares
Stock Option (Right to Buy) $ 18.75 10/26/2005   A   111,000     (5) 12/31/2005 Common Stock 111,000 (6) 111,000 D  
Stock Option (Right to Buy) $ 12.69 10/26/2005   A   25,000     (7) 10/26/2012 Common Stock 25,000 (8) 136,000 D  

Reporting Owners

Reporting Owner Name / Address Relationships
 Director  10% Owner  Officer  Other
LEPOFSKY ROBERT
C/O BROOKS AUTOMATION, INC.
15 ELIZABETH DRIVE
CHELMSFORD, MA 01824
  X      

Signatures

 /s/ Lynda M. Avallone as Attorney-in-Fact for Robert J. Lepofsky   10/28/2005
**Signature of Reporting Person Date

Explanation of Responses:

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
(1) Received in exhange for 255,073 shares of Helix Technology Corporation common stock in connection with the merger of Helix Technology Corporation and a wholly-owned subsidiary of Brooks Automation, Inc. (the "Merger"). On the effective date of the Merger, the closing price of Helix Technology Corporation's common stock was $13.96 per share, and the closing price of Brooks Automation, Inc.'s common stock was $12.69 per share.
(2) Received in the Merger in exchange for 1,955 shares of Helix Technology Corporation common stock.
(3) Received in the Merger in exchange for 40,000 shares of Helix Technology Corporation common stock.
(4) The reporting person disclaims beneficial ownership of these shares.
(5) Received in the Merger in exchange for a stock option to acquire 100,000 shares of Helix Technology Corporation common stock for $20.8125 per share.
(6) Received in the Merger in exchange for a stock option to acquire Helix Technology Corporation common stock granted on February 11, 1999. This option becomes exercisable with respect to 25% of such shares subject to the option on each anniversary of the date of grant.
(7) This option becomes exercisable with respect to 5,000 shares subject to the option on each anniversary of the date of grant, beginning on the first anniversary, such that the option becomes fully exercisable as of the fifth anniversary of the date of grant.
(8) No amount was paid upon grant of the option. The reporting person will pay for the shares upon exercise of the option pursuant to the price listed in Column 2.

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