SC TO-I/A

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

AMENDMENT NO. 2
SCHEDULE TO
TENDER OFFER STATEMENT

under Section 14(d)(1) or Section 13(e)(1) of the Securities Exchange Act of 1934

BROOKS AUTOMATION, INC.

(Name Of Subject Company (Issuer))

BROOKS AUTOMATION, INC.

(Name of Filing Persons (Offeror))

Common Stock
Rights to Purchase Common Stock
(Title of Class of Securities)

114340102
(CUSIP Number of Class of Securities)

Thomas S. Grilk
Senior Vice President, General Counsel and Secretary
Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, Massachusetts 02184
(978)262-2400
(Name, address and telephone number of person authorized to receive notices and communications on behalf of filing persons)

with copies to:

David B. Walek, Esq.
Ropes & Gray LLP
One International Place
Boston, Massachusetts 02110
(617) 951-7000

CALCULATION OF FILING FEE

Transaction Valuation*	Amount Of Filing Fee**
$115,140,000	$3,534.80

* Estimated solely for purposes of calculating the filing fee pursuant to Rules 0-11 under the Securities Exchange Act of 1934, as amended, based on the product of (x) $19.00, the maximum tender offer price and (y) 6,060,000, the maximum number of shares that will be purchased in the tender offer described in this Schedule TO.

** The amount of the filing fee, calculated in accordance with Rule 0-11(b) of the Securities Exchange Act of 1934, as amended, equals $30.70 per million of the aggregate amount of transaction value.

þ Check the box if any part of the fee is offset as provided by Rule 0-11(a)(2) and identify the filing with which the offsetting fee was previously paid. Identify the previous filing by registration statement number, or the Form or Schedule and the date of its filing.

Amount Previously Paid:	$3,534.80
Form or Registration No.:	005-45079
Filing Party:	Brooks Automation, Inc.
Date Filed:	June 1, 2007

o Check the box if the filing relates solely to preliminary communications made before the commencement of a tender offer.

Check the appropriate boxes below to designate any transactions to which the statement relates:

o third-party tender offer subject to Rule 14d-1.

þ issuer tender offer subject to Rule 13e-4.

o going-private transaction subject to Rule 13e-3.

o amendment to Schedule 13D under Rule 13d-2.

Check the following box if the filing is a final amendment reporting the results of the tender offer:   þ

     This amendment supplements the Tender Offer Statement on Schedule TO relating to a tender offer by Brooks Automation, Inc (“Brooks” or the “Company”), to purchase up to 6,060,000 shares of its common stock, par value $.01 per share, at a price not more than $19.00 nor less than $16.50 per share, to the seller in cash, without interest, upon the terms and subject to the conditions set forth in the offer to purchase, dated June 1, 2007 (the “Offer to Purchase”) and the accompanying letter of transmittal (the “Letter of Transmittal”), which together, as amended and supplemented from time to time, constitute the tender offer.

     This final amendment to Schedule TO-I is intended to satisfy the reporting requirements of Rule 13e-4(c)(1) and Rule 13e-4(c)(4) of the Securities Exchange Act of 1934, as amended. The information on the Schedule TO filed on June 1, 2007 and amended on June 29, 2007, including all schedules and annexes thereto, is hereby expressly incorporated by reference into this Amendment No. 2, except that such information is hereby amended and supplemented to the extent specifically provided herein. Capitalized terms used herein and not otherwise defined shall have the meanings given to them in the Offer to Purchase.

ITEM 11. ADDITIONAL INFORMATION

Item 11 of the Schedule TO is hereby amended and supplemented to add the following:

     At 12:56 pm on July 5, 2007 the Company issued a press release announcing the final results of the Offer, which expired at 11:59 p.m., New York City time on Thursday, June 28. A copy of the press release is filed as Exhibit (a)(5)(D) to this Schedule TO and is incorporated herein by reference.

ITEM 12. EXHIBITS

     The information contained in Item 12 of the Schedule TO and the Exhibit Index is hereby amended and supplemented to add the following:

Exhibit
Number	Description
(a)(5)(D)	Press Release issued by Brooks Automation, Inc. on July 5, 2007.

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SIGNATURES

     After due inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

	Brooks Automation, Inc.
Dated: July 5, 2007	By:	/s/ Thomas S. Grilk
		Name:	Thomas S. Grilk
		Title:	Senior Vice President, General Counsel and Secretary

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EXHIBIT INDEX

Exhibit No.	Description
(a)(1)(A)	Offer to Purchase dated June 1, 2007.*
(a)(1)(B)	Form of Letter of Transmittal.*
(a)(1)(C)	Form of Notice of Guaranteed Delivery (including Guidelines of the Internal Revenue Service for Certification of Taxpayer Identification Number on substitute Form W-9).*
(a)(1)(D)	Form of Letter to Brokers, Dealers, Banks, Trust Companies and Other Nominees.*
(a)(1)(E)	Form of Letter to Clients for Use by Brokers, Dealers, Banks, Trust Companies and Other Nominees.*
(a)(5)(A)	Press Release issued on May 31, 2007.*
(a)(5)(B)	Form of Summary Advertisement.*
(a)(5)(C)	Press Release issued on June 29, 2007.**
(a)(5)(D)	Press Release issued on July 5, 2007.
(d)(1)	1995 Employee Stock Purchase Plan, as amended (incorporated herein by reference to Exhibit 10.15 of the Company’s annual report on Form 10-K for the fiscal year ended September 30, 2006, filed on December 14, 2006).
(d)(2)	Amended and Restated 2000 Equity Incentive Plan (incorporated herein by reference to Exhibit 10.1 of the Company’s current report on Form 8-K, filed on March 7, 2006).
(d)(3)	1998 Employee Equity Incentive Plan (incorporated herein by reference to the Company’s quarterly report on Form 10-Q for the quarterly period ended March 31, 2000 (SEC Accession No. 0000950135-00-002803), filed on May 15, 2000).
(d)(4)	1993 Non-Employee Director Stock Option Plan (incorporated herein by reference to the Company’s registration statement on Form S-8 (Registration No. 333-22717), filed on March 4, 1997).
(d)(5)	1992 Combination Stock Option Plan (incorporated herein by reference to the Company’s registration statement on Form S-8 (Registration No. 333-07313), filed on July 1, 1996).
(d)(6)	Helix Technology Corporation 1996 Equity Incentive Plan (incorporated herein by reference to Exhibit 4.1 of the Company’s registration statement on Form S-8 (Registration No. 333-129724), filed on November 16. 2005).
(d)(7)	Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors (incorporated herein by reference to Exhibit 4.2 of the Company’s registration statement on Form S-8 (Registration No. 333-129724), filed on November 16. 2005).
(d)(8)	Helix Technology Corporation 1981 Employee Stock Option Plan (incorporated herein by reference to Exhibit 4.3. of the Company’s registration statement on Form S-8 (Registration No. 333-129724), filed on November 16. 2005).

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(d)(9)	PRI Automation, Inc. 2000 Stock Option Plan (incorporated herein by reference to Exhibit 10.3 of PRI Automation, Inc.’s Registration Statement on Form S-8 (Registration No. 333-33894), filed on April 3, 2000).
(d)(10)	PRI Automation, Inc. 1997 Non-Incentive Stock Option Plan (incorporated herein by reference to Exhibit 10.2 of PRI Automation, Inc.’s annual report on Form 10-K for the annual period ended September 30, 2000 (SEC Accession No. 0000912057-00-054410), filed on December 21, 2000).
(d)(11)	PRI Automation, Inc. 1994 Incentive and Non-Qualified Stock Option Plan (incorporated herein by reference to Exhibit 4.3 of PRI Automation, Inc.’s Registration Statement on Form S-8 (Registration No. 333-25217), filed on April 15, 1997).
(d)(12)	Second Amended and Restated Employment Agreement, dated as of October 18, 2006, by and between the Company and Edward C. Grady (incorporated herein by reference to Exhibit 10.1 to the Company’s current report on Form 8-K, filed on October 20, 2006).
(d)(13)	Employment Agreement, dated as of December 8, 2006, by and between the Company and Robert Woodbury (incorporated herein by reference to Exhibit 10.08 to the Company’s annual report on Form 10-K for the fiscal year ended September 30, 2006, filed on December 14, 2006).
(d)(14)	Employment Agreement, dated as of October 24, 2005, by and between the Company and Thomas S. Grilk (incorporated herein by reference to Exhibit 10.09 to the Company’s annual report on Form 10-K for the fiscal year ended September 30, 2006, filed on December 14, 2006)
(d)(15)	Employment Agreement, dated as of October 26, 2005, by and between the Company and James Gentilcore (incorporated herein by reference to Exhibit 10.10 to the Company’s annual report on Form 10-K for the fiscal year ended September 30, 2006, filed on December 14, 2006).
(d)(16)	Employment Agreement, dated as of October 26, 2005, by and between the Company and Robert Anastasi (incorporated herein by reference to Exhibit 10.12 to the Company’s annual report on Form 10-K for the fiscal year ended September 30, 2006, filed on December 14, 2006).
(d)(17)	Rights Agreement dated July 23, 1997 (incorporated by incorporated by reference to Exhibit No. 1 to the Company’s Registration Statement on Form 8-A, filed on August 7, 1997).
(d)(18)	Amendment No. 1 to Rights Agreement between the Company and the Rights Agent (incorporated herein by reference to Exhibit 4.03 of the Company’s annual report on Form 8-K for the fiscal year ended September 30, 2006, filed on June 4, 2002).
(d)(19)	Amendment No. 2 to Rights Agreement between the Company and the Rights Agent (incorporated herein by reference to the Company’s registration statement on Form 8-A/A filed on June 4, 2002).
(d)(20)	Amendment No. 3 to Rights Agreement between the Company and the Rights Agent (incorporated herein by reference to Exhibit 99.4 of the Company’s registration statement on Form 8-A/A, filed on July 11, 2005).

*	Filed with the Company’s Schedule TO on June 1, 2007.
**	Filed with the Amendment No. 1 to the Company’s Schedule TO on June 29, 2007.

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EX-99.(A)(5)(D)

Exhibit (a)(5)(D)

Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, MA 01824 Tel (978) 262-2400
Fax (978) 262-2500
www.brooks.com

Contact:
Mark Chung
Brooks Automation, Inc.
Telephone: (978) 262-2459
mark.chung@brooks.com

Brooks Automation Announces Final Results of Tender Offer

CHELMSFORD, MA, July 5, 2007 — Brooks Automation, Inc. (Nasdaq: BRKS) today announced the final results of its modified “Dutch Auction” tender offer which expired at 11:59 p.m., Eastern Daylight Time, on June 28, 2007. In accordance with the terms and conditions of the tender offer the Company has accepted for purchase 6,060,000 shares of its common stock at a purchase price of $18.20 per share, for a total cost of approximately $110.3 million. The shares accepted for purchase represent approximately 8% of the shares of common stock outstanding. The total shares tendered before proration was approximately 7,400,000 common shares. Since the offer was oversubscribed, the number of shares that Brooks accepted for purchase from each tendering shareholder was prorated, based upon the proration procedures described in the Offer to Purchase mailed to shareholders and certain other limited exceptions. Shareholders who validly tendered shares at a price equal to or below $18.20 per share have had approximately 82% of those shares accepted for purchase. The depositary will promptly issue payment for the shares accepted for purchase in the tender. Any shares properly tendered and not properly withdrawn, but not purchased, will be returned promptly to stockholders by the depositary. Brooks has financed the tender offer with available cash on hand.

About Brooks Automation, Inc.
Brooks is a leading worldwide provider of automation solutions and integrated subsystems to the global semiconductor and related industries. The company’s advanced offerings in hardware, software and services can help customers improve manufacturing efficiencies, accelerate time-to-market and reduce cost of ownership. Brooks products and global services are used in virtually every semiconductor fab in the world as well as in a number of diverse industries outside of semiconductor manufacturing. For more information, visit http://www.brooks.com.

Safe Harbor Statement under Section 21E of the Securities Exchange Act of 1934.

Some statements in this release may constitute forward-looking statements made under Section 21E of the Securities Exchange Act of 1934. These statements are neither promises nor guarantees but involve risks and uncertainties, both known and unknown, that could cause Brooks’ financial and business results to differ materially from our expectations. They are based on the facts known to management at the time they are made. These forward-looking statements include statements regarding our intention to purchase shares of the Company’s common stock and the manner in which that program will be affected. Factors that could cause results to differ from our expectations include the following: delays in effecting the repurchase plan described above, fluctuations in the price for our common stock , our dependence on the cyclical semiconductor industry; the possibility of downturns in market demand for electronics; continuing uncertainties in global political and economic conditions, especially arising out of conflict in the Middle East; and other factors and other risks that we have described in our filings with the Securities and Exchange Commission, including but not limited to Brooks’ Annual Report on Forms 10-K and 10-K/A, current reports on Form 8-K and our quarterly reports on Form 10-Q. As a result we can provide no assurance that our future results will not be materially different from those projected. Brooks expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any such statement to reflect any change in our expectations or any change in events, conditions or circumstances on which any such statement is based.