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 *
KHOURY AMIN J
   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)
04/12/2006
(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 04/12/2006   A   5,000 A (1) 7,220 D  

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
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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
Non-Qualified Stock Option (right to buy) (2) $ 18.72 04/12/2006   D     10,000 10/01/2004(3) 07/01/2011 Common Stock 10,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (4) $ 23.67 04/12/2006   D     10,000 07/01/2003(5) 07/01/2012 Common Stock 10,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (6) $ 34.65 04/12/2006   D     15,000 05/13/2003(5) 05/13/2012 Common Stock 15,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (7) $ 45.77 04/12/2006   D     5,000 07/02/2002(5) 07/02/2011 Common Stock 5,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (8) $ 61.75 04/12/2006   D     5,000 07/03/2001(5) 07/03/2010 Common Stock 5,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (9) $ 39.75 04/12/2006   D     20,000 05/31/2001(10) 05/31/2010 Common Stock 20,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (11) $ 26.75 04/12/2006   D     4,000 07/01/2000(5) 07/01/2009 Common Stock 4,000 (1) 0 D  
Non-Qualified Stock Option (right to buy) (12) $ 20 04/12/2006   D     2,000 07/01/1998(5) 07/01/2007 Common Stock 2,000 (1) 0 D  

Reporting Owners

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

Signatures

 /s/ By Thomas S. Grilk Attorney-in-Fact for Amin J. Khoury   04/12/2006
**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) On the date indicated in Table I, Column 2 and Table II, Column 3, the issuer cancelled, pursuant to a Restricted Stock and Option Cancellation Agreement, options granted to the reporting person. In exchange for the options and for $.01 per share, the reporting person received 5000 shares of restricted stock.
(2) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on July 1, 2004.
(3) The cancelled option provided for vesting in 16 equal quarterly increments beginning on the date set forth in Table II, Column 6.
(4) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on July 1, 2002.
(5) The cancelled option provided for vesting in five equal annual increments commencing on the date set forth in Table II, Column 6.
(6) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on May 13, 2002.
(7) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on July 2, 2001.
(8) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on July 3, 2000.
(9) Cancellation of option to buy the number of shares of Common Stock set forth in Table II, Column 7, granted to the reporting person on May 31, 2000.
(10) The cancelled option provided for vesting in four equal annual increments commencing on the date set forth in Table II, Column 6.
(11) Cancellation of option to buy 4000 shares of Common Stock, granted to the reporting person on July 1, 1999. The original grant was for 5000 shares. On May 1, 2001, the reporting person exercised his option to purchase 1000 of the 5000 shares. 4000 shares remain outstanding with respect to this option.
(12) Cancellation of option to buy 2000 shares of Common Stock, granted to the reporting person on July 1, 1999. The original grant was for 5000 shares. On March 1, 2000, the reporting person exercised his option to purchase 2000 of the 5000 shares. On May 1, 2001, the reporting person exercised his option to purchase 1000 shares. 2000 shares remain outstanding with respect to this option.

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