SEC Form 4

FORM 4		UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* KHOURY AMIN J (Last) (First) (Middle) C/O BROOKS AUTOMATION, INC. 15 ELIZABETH DRIVE (Street) CHELMSFORD MA 01824 (City) (State) (Zip)	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)
	3. Date of Earliest Transaction (Month/Day/Year) 04/12/2006
	4. If Amendment, Date of 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

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

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 Securities Underlying Derivative Security (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: 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

Explanation of Responses:

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.

Remarks:

	/s/ By Thomas S. Grilk Attorney-in-Fact for Amin J. Khoury	04/12/2006
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* 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).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB Number.