S-8

As filed with the Securities and Exchange Commission on November 15, 2005

Registration No. 333-____________

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM S-8

REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933

BROOKS AUTOMATION, INC.

(Exact Name of Registrant as Specified in its Charter)

Delaware

(State or Other Jurisdiction of Incorporation or Organization)

04-3040660

(I.R.S. Employer Identification Number)

15 Elizabeth Drive, Chelmsford, MA 01824

(Address of Principal Executive Offices)

Helix Technology Corporation 1996 Equity Incentive Plan
Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors
Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended

(Full Title of the Plans)

Thomas S. Grilk
Senior Vice President, General Counsel and Secretary
Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, MA 01824

(Name and Address of Agent for Service)

(978) 721-3371

(Telephone Number, Including Area Code for Agent for Service)

CALCULATION OF REGISTRATION FEE

			Proposed Maximum		Proposed		Amount of
Title of Securities to be	Amount to be		Offering Price Per		Maximum Aggregate		Registration
Registered	Registered (1)		Share (2)		Offering Price (2)		Fee (2)
Helix Technology Corporation 1996 Equity Incentive Plan		721,080	$	13.095	$	9,442,542.60	$	1,111.39
Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors		26,640	$	13.095	$	348,850.80	$	41.06
Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended		22,200	$	13.095	$	290,709.00	$	34.22

(1)

This Registration Statement covers an aggregate of 769,920 shares of the Registrant’s common stock, par value $.01 per share (the “Common Stock”), that may be issued pursuant to awards granted under the equity plans identified above (collectively, the “Plans”). Pursuant to Rule 416(a) under the Securities Act of 1933, this registration statement also covers such additional shares of Common Stock as may be issued in the event of a stock dividend, stock split, recapitalization or other similar transaction. In addition, this registration statement covers related rights to purchase Series A Junior Participating Preferred Stock, par value $.01 per share, registered on a Form 8-A filed with the Securities and Exchange Commission on August 7, 1997 (the “Preferred Stock Purchase Rights”). No separate consideration will be received for the Preferred Stock Purchase Rights, which will initially trade together with the Common Stock.

(2)

Estimated solely for the purpose of determining the registration fee pursuant to Rule 457(h) on the basis of the average of the high and low sale prices of the Common Stock on the Nasdaq National Market on November 9, 2005.

TABLE OF CONTENTS

	Item 3. Incorporation of Documents by Reference.
	Item 4. Description of Securities.
	Item 5. Interests of Named Experts and Counsel.
	Item 6. Indemnification of Directors and Officers
	Item 7. Exemption from Registration Claimed.
	Item 8. Exhibits.
	Item 9. Undertakings
SIGNATURES
EXHIBIT INDEX
Helix Technology Corporation 1996 Equity Incentive Plan
Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors
Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
Consent of Thomas S. Grilk, Esq.
Consent of PricewaterhouseCoopers LLP

PART II

INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3. Incorporation of Documents by Reference.

	The Registrant incorporates by reference the following documents filed with the Commission:
(a)	the Registrant’s Annual Report on Form 10-K for the fiscal year ended September 30, 2004;
(b)	the Registrant’s Proxy statement on Schedule 14A filed with the SEC on January 6, 2005;
(c)	the Registrant’s Quarterly Reports on Form 10-Q for the quarters ended December 31, 2004, March 31, 2005 and June 30, 2005
(d)	the Registrant’s Current Reports on Form 8-K filed with the Commission on December 28, 2004, February 23, 2005, April 29, 2005, July 11, 2005, August 24, 2005 and October 27, 2005;
(e)	the description of the Common Stock which is contained in the Registrant’s Registration Statement on Form 8-A filed by the Registrant under Section 12 of the Securities Exchange Act of 1934 on January 27, 1995, including any amendments or reports filed for the purpose of updating such description; and
(f)	the description of the Preferred Stock Purchase Rights which is contained in the Registrant’s Registration Statement on Form 8-A filed by the Registrant under Section 12 of the Securities Exchange Act of 1934 on August 7, 1997, including any amendments or reports filed for the purpose of updating such description.

         In addition, all documents subsequently filed by the Registrant pursuant to Section 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934, prior to the filing of a post-effective amendment which indicates that all securities offered have been sold or which deregisters all securities then remaining unsold under this Registration Statement, shall be deemed to be incorporated by reference in this Registration Statement and to be a part hereof from the date of filing of such documents. Any statement contained herein or in a document incorporated or deemed to be incorporated by reference herein shall be deemed to be modified or superceded for purposes of this Registration Statement to the extent that a statement contained herein or in any other subsequently filed document which also incorporated or is deemed to be incorporated by reference herein modifies or supercedes such earlier statement. Any statement so modified or superceded shall not be deemed, except as so modified or superceded, to constitute part of this Registration Statement.

Item 4. Description of Securities.

          Not applicable.

Item 5. Interests of Named Experts and Counsel.

          The legality of the shares of Common Stock being registered pursuant to this Registration Statement will be passed upon for the Registrant by Thomas S. Grilk, Esq., General Counsel of the Registrant. Mr. Grilk holds options to purchase Common Stock.

Item 6. Indemnification of Directors and Officers

     The Registrant is incorporated under the laws of the State of Delaware. Section 102 of the General Corporation Law of the State of Delaware (the “DGCL”) provides that a Delaware corporation may eliminate the personal liability of directors of a corporation to the corporation or its stockholders for monetary damages for a breach of fiduciary duty as a director, except where the director breached his duty of loyalty, failed to act in good faith, engaged in intentional misconduct or knowingly violated a law, authorized the payment of a dividend or approved a stock repurchase in violation of Delaware corporate law or obtained an improper personal benefit.

     Section 145 of the DGCL provides that a Delaware corporation may indemnify any persons who were, are or are threatened to be made parties to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative (other than an action by or in the right of such corporation), by reason of the fact that such person is or was an officer, director, employee or agent of such corporation, or is or was serving at the request of such corporation as a director, officer, employee or agent of another corporation or enterprise. The indemnity may include

1

expenses (including attorneys’ fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding, provided that such person acted in good faith and in a manner he reasonably believed to be in or not opposed to the corporation’s best interests and, with respect to any criminal action or proceeding, had no reasonable cause to believe that his conduct was illegal.

     Section 145 further authorizes a corporation to purchase and maintain insurance on behalf of any person who is or was a director, officer, employee or agent of the corporation, or is or was serving at the request of the corporation as a director, officer, employee or agent of another corporation or enterprise, against any liability asserted against him and incurred by him in any such capacity, arising out of his status as such, whether or not the corporation would otherwise have the power to indemnify him under Section 145.

     The Registrant’s certificate of incorporation provides that its directors shall not be liable to the Registrant or its stockholders for monetary damages for breach of fiduciary duty as a director, except that directors will be liable to the extent permitted by applicable law for breach of the director’s duty of loyalty to the stockholders, actions or omissions not taken in good faith or that involve intentional misconduct, pursuant to Section 174 of the DGCL or for any transaction from which the director derived an improper benefit. The Registrant’s certificate of incorporation provides that the Registrant may indemnify its directors and officers to the full extent permitted by the laws of the State of Delaware. In addition, the Registrant’s bylaws provide that the Registrant may indemnify its officers and directors to the fullest extent permitted by applicable law.

     All of the Registrant’s directors and officers are covered by insurance policies maintained by the Registrant against specified liabilities for actions taken in their capacities as such, including liabilities under the Securities Act, as amended. In addition, the Registrant has entered into indemnification agreements with each of its directors and executive officers that provide for indemnification and expense advancement to the fullest extent permitted under the DGCL.

Item 7. Exemption from Registration Claimed.

          Not applicable.

Item 8. Exhibits.

          The following exhibits are filed as part of or incorporated by reference into this Registration Statement:

4.1	Helix Technology Corporation 1996 Equity Incentive Plan.
4.2	Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.
4.3	Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended.
5.1	Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.
23.1	Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.
23.2	Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit 5.1 to this Registration Statement).
24.1	Power of Attorney (included on signature pages of this Registration Statement).

Item 9. Undertakings

(a) The Registrant hereby undertakes:

     (1) To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

          (i) To include any prospectus required by Section 10(a)(3) of the Securities Act of 1933;

          (ii) To reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of

2

securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20 percent change in the maximum aggregate offering price set forth in the “Calculation of Registration Fee” table in the effective registration statement;

          (iii) To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the Registration Statement;

          provided, however, that paragraphs (i) and (ii) above do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in periodic reports filed with or furnished to the Securities and Exchange Commission by the registrant pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in the registration statement.

     (2) That, for the purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

     (3) To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(b) The undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act of 1933, each filing of the registrant’s annual report pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan’s annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(c) Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the registrant pursuant to the foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act of 1933 and will be governed by the final adjudication of such issue.

3

SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8, and has duly caused this registration statement on Form S-8 to be signed on its behalf by the undersigned, thereunto duly authorized in the City of Chelmsford, Massachusetts on November 15, 2005.

BROOKS AUTOMATION, INC.
By:	/s/ Edward C. Grady
Edward C. Grady
Chief Executive Officer and Director

     We, the undersigned officers and directors of Brooks Automation, Inc., hereby severally constitute and appoint Thomas S. Grilk, Robert W. Woodbury, Jr. and Edward C. Grady, and each of them singly, our true and lawful attorneys-in-fact, with full power to them in any and all capacities, to sign any and all amendments to this Registration Statement on Form S-8 (including any post-effective amendments), and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact may do or cause to be done by virtue hereof.

     Pursuant to the requirements of the Securities Act of 1933, this registration statement has been signed by the following persons in the capacities indicated as of November 15, 2005.

Signatures	Title
/s/ Edward C. Grady EDWARD C. GRADY	Chief Executive Officer and Director (Principal Executive Officer)
/s/ Robert W. Woodbury, Jr. ROBERT W. WOODBURY, JR	Senior Vice President and Chief Financial Officer (Principal Financial and Accounting Officer)
/s/ A. Clinton Allen A. CLINTON ALLEN	Director
/s/ Roger D. Emerick ROGER D. EMERICK	Director
/s/ Amin J. Khoury AMIN J. KHOURY	Director

Signatures	Title
/s/ Joseph R. Martin JOSEPH R. MARTIN	Director
/s/ John K. McGillicuddy JOHN K. MCGILLICUDDY	Director
/s/ Robert J. Therrien ROBERT J. THERRIEN	Director
/s/ Robert J. Lepofsky ROBERT J. LEPOFSKY	Director
/s/ Alfred Woollacott, III ALFRED WOOLLACOTT, III	Director
/s/ Mark S. Wrighton MARK S. WRIGHTON	Director

EXHIBIT INDEX

4.1	Helix Technology Corporation 1996 Equity Incentive Plan.
4.2	Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.
4.3	Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
5.1	Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.
23.1	Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.
23.2	Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit 5.1 to this Registration Statement).
24.1	Power of Attorney (included on signature pages of this Registration Statement).

EX-4.1

Exhibit 4.1

HELIX TECHNOLOGY CORPORATION

1996 EQUITY INCENTIVE PLAN

(As Amended and Restated)

1. Purpose and History

The purpose of the Helix Technology Corporation 1996 Equity Incentive Plan (the “Plan”) as amended and restated is to attract and retain key employees, consultants, and directors of the Company and its Affiliates, to provide an incentive for them to achieve long-range performance goals, and to enable them to participate in the long-term growth of the Company.

The Plan was originally established in 1996, and is hereby being amended and restated. The Company has also maintained the Helix Technology Corporation Stock Option Plan for Non-Employee Directors (the “Directors’ Plan”). As part of this amendment and restatement of the Plan, the non-employee directors of the Company shall become eligible to participate in this Plan, any remaining shares of Common Stock available for grant under the Directors’ Plan shall become available for issue under this Plan, and upon approval of the stockholders of this amendment and restatement no further options shall be granted under the Directors’ Plan. Any options that are outstanding under the Directors’ Plan as of the date of stockholder approval of this amendment and restatement shall continue to be governed by the terms of the Directors’ Plan and the relevant grant agreements except as otherwise specifically provided in this Plan.

2. Definitions

“Affiliate” means any business entity in which the Company owns directly or indirectly 50% or more of the total voting power or has a significant financial interest as determined by the Committee.

“Award” means any Option, Stock Appreciation Right, Restricted Stock, Restricted Stock Unit, or Foreign National Award granted under the Plan.

“Board” means the Board of Directors of the Company.

“Code” means the Internal Revenue Code of 1986, as amended from time to time, or any successor law.

“Committee” means one or more committees each comprised of not less than three members of the Board appointed by the Board to administer the Plan or a specified portion thereof. If a Committee is authorized to grant Awards to a Reporting Person or a Covered Employee, each member shall be a “disinterested person” or the equivalent within the meaning of applicable Rule 16b-3 under the Exchange Act or an “outside director” or the equivalent within the meaning of Section 162(m) of the Code, respectively.

“Common Stock” or “Stock” means the Common Stock, $1.00 par value, of the Company.

“Company” means Helix Technology Corporation.

“Covered Employee” means a “covered employee” within the meaning of Section 162(m) of the Code.

“Designated Beneficiary” means the beneficiary designated by a Participant, in a manner determined by the Committee, to receive amounts due or exercise rights of the Participant in the event of the Participant’s death. In the absence of an effective designation by a Participant, “Designated Beneficiary” means the Participant’s estate.

“Exchange Act” means the Securities Exchange Act of 1934, as amended from time to time, or any successor law.

“Fair Market Value” means, with respect to Common Stock or any other property, the fair market value of such property as determined by the Committee in good faith or in the manner established by the Committee from time to time.

-1-

“Foreign National Award” — See Section 9(i).

“Incentive Stock Option” — See Section 6(a).

“Nonstatutory Stock Option” — See Section 6(a).

“Option” — See Section 6(a).

“Participant” means a person selected by the Committee to receive an Award under the Plan.

“Performance Goals” means with respect to any Performance Period, one or more objective performance goals based on one or more of the following objective criteria established by the Committee prior to the beginning of such Performance Period or within such period after the beginning of the Performance Period as shall meet the requirements to be considered “pre-established performance goals” for purposes of Code Section 162(m): (i) increases in the price of the Common stock, (ii) market share, (iii) sales, (iv) revenue, (v) return on equity, assets, or capital, (vi) economic profit (economic value added), (vii) total shareholder return, (viii) costs, (ix) expenses, (x) margins, (xi) earnings or earnings per share, (xii) cash flow, (xiii) customer satisfaction, (xiv) operating profit, (xv) research and development, (xvi) product development, (xvii) manufacturing, or (xviii) any combination of the foregoing, including without limitation, goals based on any of such measures relative to appropriate peer groups or market indices. Such Performance Goals may be particular to a Participant or may be based, in whole or in part, on the performance of the division, department, line of business, subsidiary, or other business unit, whether or not legally constituted, in which the Participant works or on the performance of the Company generally.

“Performance Period” means the period of service designated by the Committee applicable to an Award subject to Section 9(l) during which the Performance Goals will be measured.

“Reporting Person” means a person subject to Section 16 of the Exchange Act.

“Restricted Period” — See Section 8(a).

“Restricted Stock” — See Section 8(a).

“Restricted Stock Unit” — See Section 8(c)

“Stock Appreciation Right” or “SAR” — See Section 7(a).

3. Administration

The Plan shall be administered by the Committee. The Committee shall determine which eligible employees, consultants, and directors will receive Awards. The Committee shall have authority to adopt, alter and repeal such administrative rules, guidelines and practices governing the operation of the Plan as it shall from time to time consider advisable, to interpret the provisions of the Plan and any Award agreement, and to remedy any ambiguities or inconsistencies therein. The Committee’s decisions shall be subject to final ratification by the full Board. To the extent permitted by applicable law, the Committee may delegate to one or more executive officers of the Company the power to make Awards to Participants who are not subject to Section 16 of the Exchange Act and all determinations under the Plan with respect thereto, provided that the Committee shall fix the maximum amount of such Awards for all such Participants and a maximum for any one Participant, and such other features of the Awards as required by applicable law.

4. Eligibility

All employees and, in the case of Awards other than Incentive Stock Options under Section 6, directors and consultants of the Company or any Affiliate, capable of contributing significantly to the successful performance of the Company, are eligible to be Participants in the Plan. Incentive Stock Options may be granted only to eligible employees of the Company or its Affiliates.

-2-

5. Stock Available for Awards

(a) Amount. Subject to adjustment under Section 5(b), Awards may be made under the Plan for up to 1,800,000 shares of Common Stock, together with all shares of Common Stock available for issue under the Directors’ Plan as of the date of the approval of this amendment and restatement by the Company’s stockholders. If any Award (including any grant under the Directors’ Plan) expires or is terminated unexercised, or is forfeited or settled in cash or in a manner that results in fewer shares outstanding than were awarded, then the shares subject to such Award, to the extent of such expiration, termination, forfeiture or decrease, shall again be available for award under the Plan. Common Stock issued through the assumption or substitution of outstanding grants from an acquired company shall not reduce the shares available for Awards under the Plan. Shares issued under the Plan may consist in whole or in part of authorized but unissued shares or treasury shares.

(b) Adjustment. In the event that the Committee determines that any stock dividend, extraordinary cash dividend, recapitalization, reorganization, merger, consolidation, split-up, spin-off, combination, exchange of shares, or other transaction affects the Common Stock such that an adjustment is required in order to preserve the benefits intended to be provided by the Plan, then the Committee (subject in the case of Incentive Stock Options to any limitation required under the Code) shall equitably adjust any or all of (i) the number and kind of shares in respect of which Awards may be made under the Plan, (ii) the number and kind of shares subject to outstanding Awards, and (iii) the exercise price with respect to any of the foregoing, and if considered appropriate, the Committee may make provision for a cash payment with respect to an outstanding Award, provided that the number of shares subject to any Award shall always be a whole number.

(c) Limit on Individual Grants. The maximum number of shares of Common Stock subject to all Awards that may be granted under this Plan to any Participant in the aggregate in any calendar year shall not exceed 200,000 shares, subject to adjustment under subsection (b). With respect to any Award settled in cash that is intended to satisfy the requirements for “performance-based compensation” (within the meaning of Section 162(m)(4)(C) of the Code), no more than $5,000,000 may be paid to any one individual with respect to each year of a Performance Period.

6. Stock Options

(a) Grant of Options. Subject to the provisions of the Plan, the Committee may grant options (“Options”) to purchase shares of Common Stock (i) complying with the requirements of Section 422 of the Code or any successor provision and any regulations thereunder (“Incentive Stock Options”), and (ii) not intended to comply with such requirements (“Nonstatutory Stock Options”). The Committee shall determine the number of shares subject to each Option and the exercise price therefor, which shall not be less than 100% of the Fair Market Value of the Common Stock on the date of grant.

(b) Terms and Conditions. Each Option shall be exercisable at such times and subject to such terms and conditions as the Committee may specify in the applicable grant or thereafter; provided that (i) no Option shall be exercisable after the expiration of ten years from the date the Option is granted, and (ii) no Option may be granted with a reload feature which provides for an automatic grant of additional or replacement options upon the exercise of an Option. The Committee may impose such conditions with respect to the exercise of Options, including conditions relating to applicable securities laws, as it considers necessary or advisable.

(c) Payment. No shares shall be delivered pursuant to any exercise of an Option until payment in full of the exercise price therefor is received by the Company. Such payment may be made in whole or in part in cash or to the extent permitted by the Committee at or after the grant of the Option, pursuant to any of the following methods: (i) by actual delivery or attestation of ownership of shares of Common Stock owned by the Participant, including vested Restricted Stock, (ii) by retaining shares of Common Stock otherwise issuable pursuant to the Option, (iii) for consideration received by the Company under a broker-assisted cashless exercise program acceptable to the Company, or (iv) for such other lawful consideration as the Committee may determine.

7. Stock Appreciation Rights

(a) Grant of SARs. Subject to the provisions of the Plan, the Committee may grant rights to receive any excess in value of shares of Common Stock over the exercise price (“Stock Appreciation Rights” or “SARs”) in tandem with an Option (at or after the award of the Option), or alone and unrelated to an Option. SARs in tandem with an Option shall terminate to the extent that the related Option is exercised, and the related Option shall terminate to the extent

-3-

that the tandem SARs are exercised. The Committee shall determine at the time of grant or thereafter whether SARs are settled in cash, Common Stock or other securities of the Company, Awards or other property.

(b) Exercise Price. The Committee shall fix the exercise price of each SAR or specify the manner in which the price shall be determined. An SAR granted in tandem with an Option shall have an exercise price not less than the exercise price of the related Option. An SAR granted alone and unrelated to an Option may not have an exercise price less than 100% of the Fair Market Value of the Common Stock on the date of the grant.

(c) Limited SARs. An SAR related to an Option, which SAR can only be exercised upon or during limited periods following a change in control of the Company, may entitle the Participant to receive an amount based upon the highest price paid or offered for Common Stock in any transaction relating to the change in control or paid during a specified period immediately preceding the occurrence of the change in control in any transaction reported in the stock market in which the Common Stock is normally traded.

8. Restricted Stock and Restricted Stock Units

(a) Grant of Restricted Stock. Subject to the provisions of the Plan, the Committee may grant shares of Common Stock subject to forfeiture (“Restricted Stock”) and determine the duration of the period (the “Restricted Period”) during which, and the conditions under which, the shares may be forfeited to the Company and the other terms and conditions of such Awards. Shares of Restricted Stock may be issued for no cash consideration or such minimum consideration as may be required by applicable law.

(b) Restrictions. Shares of Restricted Stock may not be sold, assigned, transferred, pledged or otherwise encumbered, except as permitted by the Committee, during the Restricted Period. Shares of Restricted Stock shall be evidenced in such manner as the Committee may determine. Any certificates issued in respect of shares of Restricted Stock shall be registered in the name of the Participant and unless otherwise determined by the Committee, deposited by the Participant, together with a stock power endorsed in blank, with the Company. At the expiration of the Restricted Period, the Company shall deliver such certificates to the Participant or if the Participant has died, to the Participant’s Designated Beneficiary.

(c) Restricted Stock Units. Subject to the provisions of the Plan, the Committee may grant the right to receive in the future shares of Common Stock subject to forfeiture (“Restricted Stock Units”) and determine the duration of the Restricted Period during which, and the conditions under which, the Award may be forfeited to the Company and the other terms and conditions of such Awards. Restricted Stock Unit Awards shall constitute an unfunded and unsecured obligation of the Company, and shall be settled in shares of Common Stock or cash, as determined by the Committee at the time of grant or thereafter. Such Awards shall be made in the form of “units” with each unit representing the equivalent of one share of Common Stock.

9. General Provisions Applicable to Awards

(a) Transferability. Except as otherwise provided in this Section 9(a), an Award (i) shall not be transferable other than as designated by the Participant by will or by the laws of descent and distribution, and (ii) may be exercised during the Participant’s lifetime only by the Participant or by the Participant’s guardian or legal representative. In the discretion of the Committee, any Award may be transferable upon such terms and conditions and to such extent as the Committee determines at or after grant, provided that Incentive Stock Options may be transferable only to the extent permitted by the Code.

(b) Documentation. Each Award under the Plan shall be evidenced by a writing delivered to the Participant specifying the terms and conditions thereof and containing such other terms and conditions not inconsistent with the provisions of the Plan as the Committee considers necessary or advisable to achieve the purposes of the Plan or to comply with applicable tax and regulatory laws and accounting principles.

(c) Committee Discretion. Each type of Award may be made alone, in addition to or in relation to any other Award. The terms of each type of Award need not be identical, and the Committee need not treat Participants uniformly. In addition to the authority granted to the Committee in Section 9(l) to make Awards to Covered Employees which qualify as “performance-based compensation” for purposes of Section 162(m) of the Code, the Company may grant Awards subject to such performance conditions (including performance-based vesting) as it shall determine in its discretion. Except as otherwise provided by the Plan or a particular Award, any determination with respect to an Award may be made by the Committee at the time of grant or at any time thereafter.

-4-

(d) Dividends and Cash Awards. In the discretion of the Committee, any Award under the Plan may provide the Participant with (i) dividends or dividend equivalents payable currently or deferred with or without interest, and (ii) cash payments in lieu of or in addition to an Award.

(e) Termination of Employment or Service. The Committee shall determine and set forth in the grant agreement evidencing the Award the effect on an Award of the disability, death, retirement or other termination of employment or service of a Participant and the extent to which, and the period during which, the Participant’s legal representative, guardian or Designated Beneficiary may receive payment of an Award or exercise rights thereunder. Unless the Committee provides otherwise in any case, a Participant’s employment or service shall have terminated for purposes of this Plan at the time the entity by which the Participant is employed or to which the Participant renders service ceases to be an Affiliate of the Company.

(f) Change in Control. In order to preserve a Participant’s rights under an Award in the event of a change in control of the Company as defined by the Committee (a “Change in Control”), the Committee in its discretion may, at the time an Award is made or at any time thereafter, take one or more of the following actions: (i) provide for the acceleration of any time period relating to the exercise or payment of the Award, (ii) provide for payment to the Participant of cash or other property with a Fair Market Value equal to the amount that would have been received upon the exercise or payment of the Award had the Award been exercised or paid upon the Change in Control, (iii) adjust the terms of the Award in a manner determined by the Committee to reflect the Change in Control, (iv) cause the Award to be assumed, or new rights substituted therefor, by another entity, or (v) make such other provision as the Committee may consider equitable to Participants and in the best interests of the Company.

(g) Loans. The Committee may not authorize the making of loans to Participants in connection with the grant or exercise of any Award under the Plan.

(h) Withholding Taxes. The Participant shall pay to the Company, or make provision satisfactory to the Committee for payment of, any taxes required by law to be withheld in respect of Awards under the Plan no later than the date of the event creating the tax liability. In the Committee’s discretion, such tax obligations may be paid in whole or in part in shares of Common Stock, including shares retained from the Award creating the tax obligation, valued at their Fair Market Value on the date of delivery. The Company and its Affiliates may, to the extent permitted by law, deduct any such tax obligations from any payment of any kind otherwise due to the Participant.

(i) Foreign National Awards. Notwithstanding anything to the contrary contained in this Plan, Awards may be made to Participants who are foreign nationals or employed or performing services outside the United States on such terms and conditions different from those specified in the Plan as the Committee considers necessary or advisable to achieve the purposes of the Plan or to comply with applicable laws.

(j) Amendment of Award. Except as provided in Section 9(k), the Committee may amend, modify or terminate any outstanding Award, including substituting therefor another Award of the same or a different type, changing the date of exercise or realization and converting an Incentive Stock Option to a Nonstatutory Stock Option, provided that the Participant’s consent to such action shall be required unless (i) the Committee determines that the action, taking into account any related action, would not materially and adversely affect the Participant, or (ii) the action is permitted by the terms of the Plan.

(k) No Repricing of Options. Notwithstanding anything to the contrary in the Plan, the Company shall not engage in any repricing of Options granted under this Plan (including those granted under the Directors’ Plan) without further stockholder approval. For this purpose, the term “repricing” shall mean any of the following or other action that has the same effect: (i) lowering the exercise price of an Option after it is granted, (ii) any other action that is treated as a repricing under generally accepted accounting principles, or (iii) canceling an Option at a time when its exercise price exceeds the fair market value of the underlying stock in exchange for another Option, Restricted Stock, or other equity of the Company, unless the cancellation and exchange occurs in connection with a merger, acquisition, spin-off, or similar corporate transaction.

(l) Code Section 162(m) Provisions. If the Committee determines at the time an Award is granted to a Participant that such Participant is, or may be as of the end of the tax year for which the Company would claim a tax deduction in connection with such Award, a Covered Employee, then the Committee may provide that the Participant’s right to receive cash, Shares, or other property pursuant to such Award shall be subject to the satisfaction of Performance Goals during a Performance Period. Prior to the payment of any Award subject to this Section 9(l), the Committee

-5-

shall certify in writing that the Performance Goals and other material terms applicable to such Award were satisfied. Notwithstanding the attainment of Performance Goals by a Covered Employee, the Committee shall have the right to reduce (but not to increase) the amount payable at a given level of performance to take into account additional factors that the Committee may deem relevant. The Committee shall have the power to impose such other restrictions on Awards subject to this Section 9(l) as it may deem necessary or appropriate to ensure that such Awards satisfy all requirements for “performance-based compensation” within the meaning of Section 162(m) of the Code.

(m) Minimum Vesting Requirements. Each Stock Option and SAR granted under the Plan shall vest in accordance with a schedule which does not permit more than one-third of each such Award to vest on each of the three succeeding anniversaries of the date of grant of the Award. Each Award of Restricted Stock or Restricted Stock Units shall vest in accordance with a schedule which does not permit such Award to vest prior to the third anniversary of the date of grant of the Award. These minimum vesting requirements shall not, however, preclude the Committee from exercising its discretion to (i) accelerate the vesting of any Award upon retirement, termination of employment by the Company, death or disability, (ii) accelerate the vesting of an Award in accordance with Section 9(f), (iii) establish a shorter vesting shedule for consultants, directors, or newly-hired employees, (iv) establish a shorter vesting schedule for Awards that are granted in exchange for or in lieu of the right to receive the payment of an equivalent amount of salary, bonus, or other cash compensation, or (v) establish a performance-based vesting schedule in accordance with Section 9(c) or Section 9(l).

10. Miscellaneous

(a) No Right To Employment. No person shall have any claim or right to be granted an Award. Neither the Plan nor any Award hereunder shall be deemed to give any employee the right to continued employment or service or to limit the right of the Company to discharge any Participant at any time.

(b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no Participant or Designated Beneficiary shall have any rights as a stockholder with respect to any shares of Common Stock to be distributed under the Plan until he or she becomes the holder thereof. A Participant to whom Common Stock is awarded shall be considered the holder of the Stock at the time of the Award except as otherwise provided in the applicable Award.

(c) Effective Date. Subject to the approval of the stockholders of the Company, the amendment and restatement of the Plan shall be effective on March 16, 2004.

(d) Amendment and Term of Plan. The Board may amend, suspend or terminate the Plan or any portion thereof at any time, subject to such stockholder approval as the Board determines to be necessary or advisable to comply with any tax or regulatory requirement. Unless terminated earlier by the Board, or extended by subsequent approval of the Company’s stockholders, the term of the Plan shall expire on April 28, 2014, and no further Awards shall be made thereafter.

(e) Governing Law. The provisions of the Plan shall be governed by and interpreted in accordance with the laws of Delaware.

This Plan, as amended and restated, was approved by the Board of Directors on March 16, 2004.

This Plan, as amended and restated, was approved by the stockholders on April 28, 2004.

-6-

EX-4.2

Exhibit 4.2

AMENDED AND RESTATED

HELIX TECHNOLOGY CORPORATION

STOCK OPTION PLAN FOR NON-EMPLOYEE DIRECTORS

1. Purpose

     The purpose of the Helix Technology Corporation Stock Option Plan for Non-Employee Directors (the “Plan”) is to attract and retain the services of experienced and knowledgeable Directors of Helix Technology Corporation (the “Corporation”) for the benefit of the Corporation and its stockholders and to provide additional incentives for such Directors to continue to serve the best interests of the Corporation and its stockholders through continuing ownership of its common stock.

2. Shares Subject to the Plan

     The total number of shares of common stock, par value $1.00 per share (the “Common Stock”), of the Corporation which may be issued pursuant to options granted under the Plan (including options granted under the Plan prior to the date of this amendment and restatement (“Prior Options”)) shall not exceed 200,000 in the aggregate (the “Shares”), subject to adjustment in accordance with Section 9 hereof. Shares for which options have been granted pursuant to the Plan, but which options have lapsed or otherwise terminated or been canceled to any extent prior to full exercise, shall become available for additional options granted under the Plan.

3. Administration of Plan

     The Plan shall be administered by the Human Resources and Compensation Committee of the Board of Directors (the “Board”) or such other committees as the Board may appoint satisfying the requirements to qualify for an exemption under Rule 16b-3 under the Securities Exchange Act of 1934 (the “Committee”). The Committee shall appoint a person (the “Plan Administrator”) to keep records of all elections of Directors and the grant, vesting and exercise of all options, and the sale or other disposition of all Shares acquired pursuant to such exercise.

     Grants of stock options under the Plan shall be made by the Committee as provided in Section 4. All questions of interpretation with respect to the Plan and options granted under it shall be determined by the Committee, and such determination shall be final and binding upon all persons having an interest in the Plan.

     The Committee shall have the power to (i) make all determinations necessary or advisable for administering the Plan, (ii) correct any defect or supply any omission or reconcile any inconsistency in the Plan or in any stock option grant in the manner and to the extent that the Committee shall deem expedient to carry it into effect, and (iii) constitute and appoint a person or persons to execute and deliver in the name and on behalf of the Corporation all such grants, agreements, instruments and other documents. It is the intent of this Plan that it operate in all events subject to approval of the Plan by the stockholders of the Corporation and that the granting and vesting of such options under it be within the authority of the Committee in accordance with the terms of this Plan, subject to the authority, discretion or power of the stockholders to fail to elect an

optionee to the Board of Directors of the Corporation, or to remove an optionee from the Board of Directors of the Corporation, or to amend or terminate this Plan.

4. Grant of Options

     (a) Annual Option Grant. Upon the conclusion of each regular annual meeting of the Corporation’s stockholders held in the year 2002 or thereafter, each Director of the Corporation who is not otherwise an employee of the Corporation or any of its subsidiaries (a “Non-Employee Director”) who will continue serving as a member of the Board thereafter and who does not hold Prior Options which have not yet vested, shall be granted an Option to acquire 2,000 shares under the Plan (the “Annual Option”).

     (b) Initial Option Grant. Any Non-Employee Director of the Corporation who is elected for the first time otherwise than at an annual meeting after the 2002 meeting shall receive an initial Option to acquire 2,000 shares under the Plan (the “Initial Option”) which shall become exercisable as of the date of the annual meeting following such Non-Employee Director’s election. The Non-Employee Director shall be eligible to receive Annual Options as described in Section 4(a).

     (c) Early Grant of Annual Options. For a Non-Employee Director elected as Director for the first time, the Committee may, in its discretion, grant the Annual Option in a year prior to which the Annual Option is earned, coincident with the regular annual meeting of the Corporation’s stockholders or at the time an Initial Option is granted, provided that any such Annual Option granted in a year earlier than which it was earned (the “Early Annual Option”) shall become vested according to the vesting schedule that would have applied to the option had the option been granted on its regularly scheduled grant date. The Committee may only grant Early Annual Options as far as four years prior to the date on which the Annual Option would have been granted had such option not been granted early.

5. Option Grant

     Each option granted under the Plan shall be a Non-Qualified Stock Option and shall be evidenced by a Grant of Option duly executed on behalf of the Corporation and shall comply with and be subject to the terms and conditions of the Plan.

6. Option Exercise Price

     The option exercise price for an option granted under the Plan shall be the fair market value of the Shares covered by the option at the time the option is granted. Fair market value shall be the mean between the high and low quoted selling prices of the Common Stock on the date the option is granted as reported on the Nasdaq National Market or, if not so quoted, on the principal national securities exchange on which the Common Stock is then listed. The option exercise price shall be subject to adjustment in accordance with Section 9 hereof.

2

7. Manner of Exercise of Options

     (a) Time and Manner of Exercise of Options.

     Options granted under the Plan shall become exercisable in full on the one-year anniversary of the date of the grant, subject to the limitations applicable to Early Annual Options set forth in Section 4(b). To the extent that the right to exercise an option has accrued and is in effect, the option may be exercised in full at one time or in part from time to time, by giving written notice to the Corporation, signed by the person or persons exercising the option, stating the number of Shares with respect to which the option is being exercised, accompanied by payment in full for such Shares. Payment may be made in whole or in part by (i) cash or cash equivalents, (ii) shares of Common Stock of the Corporation already owned for a period of at least six months, or not acquired directly or indirectly from the Corporation by the person exercising the option, valued at fair market value as defined above on the business day immediately prior to the date of exercise, (iii) delivery (on a form prescribed by the Committee) of an irrevocable direction to a securities broker approved by the Corporation to sell all or part of the shares of Common Stock being purchased under the Plan and to deliver all or part of the sales proceeds to the Corporation, or (iv) such other form of payment which the Committee determines to be acceptable and consistent with applicable laws, regulations and rules.

     (b) Taxes.

     The optionee shall pay to the Corporation, or make provision satisfactory to the Committee for payment of, any taxes required by law to be withheld in respect of any option granted under the plan no later than the date of the event creating the tax liability. In the Committee’s discretion, the minimum statutory withholding obligations, based on the minimum statutory withholding rates for federal and state tax purposes, may be paid in whole or in part in Shares of Common Stock retained from the exercise of the option, valued at the fair market value of the Common Stock on the date of exercise.

     (c) Term of Options

     The Expiration Date for each option shall be the earlier of (i) the 10^th anniversary of the date of grant or, (ii) the date 12 months after the termination of such Non-Employee Director’s service as a director for any reason.

8. Options Not Transferable

     The right of an optionee to exercise an option granted to him or her under the Plan and any interest therein or in the Shares received upon exercise shall be assignable or transferable by such optionee in a respect other than by will or the laws of descent and distribution only at the discretion of the Board, and any such option shall be exercisable during the lifetime of such optionee only by him or her except as expressly permitted by the Board. Any option granted under the Plan shall become null and void and shall be without further force or effect upon the bankruptcy of the optionee, or upon any attempted assignment or transfer of such option or any interest therein (except as provided in the preceding sentence), including, without limitation, any purported assignment, whether voluntary or by operation of law, pledge, hypothecation or other disposition, attachment, trustee process or similar process, whether legal or equitable with respect to such option or any interest therein.

3

9. Adjustments Upon Changes in Capitalization

     In the event that the outstanding shares of the Common Stock of the Corporation are changed into or exchanged for a different number or kind of shares or other securities of the Corporation or of another corporation by reason of any reorganization, merger, consolidation, recapitalization, reclassification, stock split-up, combination of shares or dividends payable in capital stock, appropriate adjustment shall be made in the number and kind of Shares as to which outstanding options, or portions thereof then unexercised shall be exercisable, to the end that the proportionate interest of the optionee shall be maintained as before the occurrence of such event; such adjustment in outstanding options shall be made without change in the total price applicable to the unexercised portion of such options and with a corresponding adjustment in the option price per Share.

10. Restrictions on Issuance of Shares

     The Corporation may impose such conditions with respect to the exercise of options, including conditions relating to applicable federal or state securities laws, as it considers necessary or advisable.

11. Termination and Amendment of Plan

     Unless sooner terminated as herein provided, or extended with the approval of the stockholders of the Corporation, the Plan shall terminate on February 20, 2012, except as to options granted prior to that date. The Board may at any time terminate the Plan or make such modifications or amendments thereto as it deems advisable; provided, however, that except as provided in Section 9 the Board may not, without the approval of the stockholders of the Corporation, (i) increase materially the benefits accruing to participants hereunder, (ii) increase the maximum aggregate number of shares for which options may be granted under the Plan or the number of shares for which an option may be granted to any optionee, (iii) modify the provisions of Section 4 regarding eligibility, (iv) extend the expiration date of the Plan, or (v) modify the provisions of Section 6 regarding the exercise price. Termination or any modification or amendment of the Plan shall not, without the consent of an optionee, materially adversely affect his or her rights under an option previously granted to him or her.

12. Scope of Amendment and Restatement

     This Plan is amended and restated as of April 24, 2002, and its terms shall apply to options granted from and after such date. Prior Options shall be governed by the terms and provisions of the Plan as in effect when such options were granted.

This Plan was approved by the Board of Directors on February 14, 1996.

This Plan was approved by the stockholders on April 24, 1996.

This Plan was amended by the Board of Directors on February 20, 2002.

This Plan as amended was approved by the stockholders on April 24, 2002.

4

EX-4.3

Exhibit 4.3

HELIX TECHNOLOGY CORPORATION

1981 EMPLOYEE STOCK OPTION PLAN

Adopted November 11, 1981
Amended April 14, 1982
Amended February 6, 1985
Amended December 9, 1987
Amended February 5, 1988
Amended April 13, 1988
Amended February 8, 1989
Amended February 13, 1992

Article 1 — Purpose

     This 1981 Stock option Plan the “Plan”) is intended to provide incentives to key employees of Helix Technology Corporation (the “Company”) and its present and future subsidiaries (as defined in Section 425(f) of the Internal Revenue Code of 1954, as amended (the “Code”)) by providing them with opportunities to purchase stock in the Company pursuant to the exercise of options. The Company intends certain options granted under the Plan which are designated as Incentive Stock Options to be “incentive stock options” complying with, and subject to, the terms and conditions of Section 422A of the Code; and with respect to those Incentive Stock Options this Plan shall be interpreted in accordance with that section of the Code, as amended, and the rules and regulations promulgated from time to time thereunder. Stock options granted hereunder which do not comply with Section 422A of the Code shall be designated as Non-Qualified Stock Options.

Article 2 — Administration of the Plan

     The Plan shall be administered by the Compensation Committee (the “Committee”) of the Board of Directors (the “Board”) of the Company. The Committee shall consist of at least two members of the Board who are not employees or officers of the Company or its subsidiaries and who are disinterested persons as defined in Securities and Exchange Commission Rule 16b-3, as amended. The Board may remove members from the Committee at any time with or without cause, or may add members to the Committee. Vacancies on the Committee, howsoever caused, shall be filled by the Board. Acts by a majority of the Committee at a meeting, or acts approved in writing by all the members of the Committee, shall be the valid acts of the Committee. Subject to the terms of the Plan, and subject to such overall policies with respect thereto as may be established from time to time by the Board, the Committee shall have authority to determine the time or times at which options shall be granted, the persons to whom options shall be granted, the number of shares covered by each option, the price per share specified in each option, the time or times when each option shall become exercisable and the duration of the exercise period or periods, and all other terms and provisions of each option and each instrument by which each option shall be evidenced.

     All determinations and interpretations made by the Committee with respect to the Plan and each option granted thereunder shall be binding and conclusive on all interested parties unless otherwise determined by the Board. The Committee may from time to time adopt such rules and regulations for carrying out the Plan as it may determine in its sole discretion. No member of the Board or the Committee shall be liable with respect to any action or determination made in good faith regarding the Plan or any option granted under it.

     In the event that the Board fails to appoint a Committee, those members of the board who are “disinterested persons” shall have all power and authority to administer the Plan. In such event, the word “Committee” wherever used herein shall be deemed to mean the “disinterested persons” on the Board unless the context requires otherwise.

Article 3 — Eligible Persons

     Options may only be granted to officers and other key employees of the Company or its subsidiaries (as defined in Section 425(f) of the Code). The granting of any option to a person shall neither entitle such person to, nor disqualify him from, participation in any other grant of options pursuant to this Plan or any other Plan. Directors who are not employees or officers of the Company or its subsidiaries shall not be eligible to receive options under the Plan.

Article 4 — Stock

     The stock subject to the options granted hereunder shall be shares of the Company’s authorized but unissued shares of Common Stock or shares of Common Stock reacquired by the Company including shares purchased in the open market (“Common Stock”). The maximum number of shares which are hereby reserved for issuance and may be issued pursuant to this Plan is 300,000 shares less such number of shares as may from time to time be issued and not forfeited pursuant to the Helix Technology Corporation 1985 Restricted Stock Plan, subject to adjustment as provided in Article 13. In the event any option granted under the Plan shall expire, terminate or be cancelled for any reason without having been exercised in full, or shall cease for any reason to be exercisable in whole or in part, the unpurchased shares subject thereto, to the extent the option ceases to be exercisable, shall again be available under the Plan.

Article 5 — Grant of Options

     Options may be granted to eligible persons in such number and at such times during the term of the Plan as the Committee shall determine.

Article 6 — Minimum Price of Options

     The price per share specified in each option granted under the Plan shall in no event be less than 100% (110% in the case of an incentive stock option granted to a 10% shareholder as defined in Section 422A(b)(6) and related sections of the Code) of the fair market value per share of Common Stock on the date the option is granted. Fair market value shall be determined by the Committee in accordance with applicable regulations but in general shall be the mean between the highest and lowest quoted selling prices in the market on the valuation date.

-2-

Article 7 — Duration of Options

     Subject to earlier termination as provided in Articles 9 and 10, each option shall expire on the date specified by the Committee, but in the case of incentive stock options such expiration date shall be not more than ten years (five years in the case of an incentive stock option granted to a 10% shareholder as defined in Section 422A(b)(6) and related sections of the Code) from its date of grant. The Committee may extend the term of any previously granted option provided that if such option is an incentive stock option it must expire not more than ten or five years from its original date of grant as provided above.

Article 8 — Exercise of Options

     Subject to the provisions of Articles 9 through 12, each option granted under the Plan shall be exercisable as follows:

A.	The option shall either be fully exercisable at the time of grant or shall become exercisable in such installments as the Committee may determine, which installments may be cumulative or noncumulative as the Committee may determine.
B.	Once an installment becomes exercisable it shall remain exercisable until expiration or termination of the option, unless otherwise specified by the Committee.
C.	Each option may be exercised from time to time, in whole or in part, up to the total number of shares with respect to which it is then exercisable.
D.	The Committee shall have the right to accelerate the date of exercise of any installment for any reason.
E.	In no event shall an Incentive Stock Option granted before January 1, 1987, hereunder be exercisable by any Optionee while there is outstanding any Incentive Stock Option which was previously granted to such Optionee to purchase stock in the Company or in a predecessor of the Company until such previously granted Incentive Stock Option is exercised in full or expires by reason of lapse of time.
F.	The aggregate fair market value (determined at the time the option is granted) of the Common Stock with respect to which Incentive Stock Options granted after December 31, 1986, are exercisable for the first time by an Optionee during any calendar year (under all Incentive Stock Option Plans of the Company and its parent and subsidiary corporations) shall not exceed $100,000.

Article 9 — Termination of Employment

     If an optionee ceases to be employed by the Company or any subsidiary, for any reason other than death, disability (within the meaning of Section 105(d)(4) of the Internal Revenue Code), or termination for cause, his options may be exercised to the extent they were exercisable

-3-

on the date he ceased to be employed by the Company or any subsidiary, but no further installments of such options will become exercisable and each such option shall terminate on the date one month following the date of such cessation (but not later than its specified expiration date). The aforesaid one month period may be extended by up to an additional two months by the Committee in its sole discretion. If an optionee’s employment is terminated for cause, all his options shall terminate immediately and be of no further force or effect. Whether authorized leaves of absences or absence on military or governmental service may constitute employment for the purposes of the Plan shall be conclusively determined by the Committee. Nothing in the Plan or in any option granted hereunder shall be deemed to give any optionee the right to continue in the employ of the Company or any of its subsidiaries or shall be deemed to interfere in any way with the right of the Company to terminate any optionee’s employment at any time and for any reason. Options granted under the Plan shall not be affected by any change of employment among the Company and its subsidiaries so long as the optionee continues to be an employee of the Company or one of its subsidiaries.

Article 10 — Disability; Death

     If an optionee becomes disabled (within the meaning of Section 105(d)(4) of the Code), his options may be exercised to the extent they were exercisable on the date he ceased to be employed by the Company or any subsidiary, but no further installments of such options will become exercisable and each such option shall terminate on the date one year following the date of such cessation of employment (but not later than its specified expiration date).

     If an optionee dies while employed by the Company or during the one month (or extended) period referred to in Article 9 or during the one year period referred to above in this Article 10, his options may be exercised to the extent they were exercisable on the date of his death (or cessation of employment, whichever first occurred), by his estate, or duly appointed representative, or beneficiary who acquires the options by will or by the laws of descent and distribution, but no further installments of such options will become exercisable and each such option shall terminate on the date one year following the date of the optionee’s death (but not later than its specified expiration date).

Article 11 — Assignability

     No option shall be assignable or transferable by the optionee except by will or by the laws of descent and distribution, and during the lifetime of the optionee each option shall be exercisable only by him.

Article 12 — Terms and Conditions of Options

     Options shall be evidenced by instruments (which need not be identical) in such forms as the Committee may from time to time approve. Such instruments shall conform to the terms and conditions set forth herein and may contain such other provisions not inconsistent with the Plan, including restrictions applicable to shares of Common Stock issuable upon exercise of options granted under the Plan, as the Committee deems advisable provided such provisions would not cause any incentive stock option to fail to qualify as an incentive stock option under Section 422A of the code. Options granted hereunder and Common Stock issuable upon the exercise of

-4-

options may not be disposed of within six months following date of grant. The Company shall not be obligated to deliver any shares unless and until, in the opinion of the Company’s counsel, all applicable Federal and state laws and regulations have been complied with, nor, in the event the outstanding common stock is at the time listed upon any stock exchange, unless and until the shares to be delivered have been listed, or authorized to be added to the list upon official notice of issuance, upon such exchange, nor unless and until all other legal matters in connection with the issuance and delivery of shares have been approved by the Company’s counsel. Without limiting the generality of the foregoing, the Company may require from the optionee such investment representation of such agreement, if any, as counsel for the Company may consider necessary in order to comply with the Securities Act of 1933. The Company shall use its best efforts to effect any such compliance and listing, and the optionee shall take any action reasonably requested by the Company in such regard.

Article 13 — Adjustments

     Upon the happening of any of the foregoing described events, an optionee’s rights under options granted hereunder shall be adjusted as hereinafter provided.

A.

In the event shares of Common Stock of the Company shall be subdivided or combined into a greater or smaller number of shares or if, upon a merger, consolidation, reorganization, split-up, liquidation, combination, recapitalization or the like of the Company, the shares of the Company’s Common Stock shall be exchanged for other securities of the Company or of another corporation, each optionee shall be entitled to purchase, subject to the terms and conditions of each individual option, such number of shares of Common Stock or amount of other securities of the Company or such other corporation as were exchangeable for the number of shares of Common Stock of the company which such optionee would have been entitled to purchase except for such action, and appropriate adjustments shall be made in the purchase price per share to reflect such subdivision, combination, or exchange; and

B.

In the event the Company shall issue any of its shares as a stock dividend upon or with respect to the shares of stock of the class which shall at the time be subject to option hereunder, each optionee upon exercising such an option shall be entitled to receive (for the purchase price paid upon such exercise) the shares as to which he is exercising his option and, in addition thereto (at no additional cost), such number of shares of the class or classes in which such stock dividend or dividends were declared or paid, and such amount of cash in lieu of fractional shares, as he would have received if he had been the holder of the shares as to which he is exercising his option at all times between the date of the granting of such option and the date of its exercise.

     Upon the happening of any of the foregoing events, the class and aggregate number of shares set forth in Article 4 hereof which are reserved for issuance pursuant to the Plan or are subject to options which have heretofore been or may hereafter be granted under the Plan shall also be appropriately adjusted to reflect the events specified in paragraphs A and B above.

-5-

     The Committee shall determine the adjustments to be made under this Article 13, and its determination shall be conclusive and binding on all interested parties.

Article 14 — Exercise of Options

     An option (or any part or installment thereof) shall be exercised by giving written notice to the Company at its principal office address, identifying the option being exercised, specifying the number of shares as to which such option is being exercised and accompanied by full payment of the purchase price thereof either (1) in United States Dollars, in cash or by certified or bank check, or (2) in shares of Common Stock of the Company owned by the optionee having a fair market value (as defined in Article 6 and determined on the business day immediately preceding the day on which the option is exercised) equal to, or a fraction of a share less than, such purchase price, or (3) in a combination of such Common Stock and cash or check. Unless the Committee otherwise determines the holder of an option shall have no rights of a stockholder with respect to the shares covered by his option until the date of issuance of a stock certificate to him for such shares. Unless the Committee otherwise determines no adjustment will be made for dividends or similar rights for which the record date occurs after the exercise of the option but prior to the date such stock certificate is issued. In no case may a fraction of a share be purchased or issued under the Plan.

Article 15 — Termination and Amendments to Plan

     The Plan was adopted by the Board on November 11, 1981, and became effective on that date subject to approval by the holders of a majority of the outstanding shares of Common Stock of the Company at the Annual Meeting of Stockholders of the Company held in 1982. The Plan as originally adopted expired on November 10, 1991 (except as to options outstanding on that date). The Plan was extended by the Board on February 13, 1992, for an additional 10 years subject to approval by the stockholders at the Annual Meeting of Stockholders of the Company held in 1992. Subject to such approval, the Plan shall expire on November 10, 2001 (except as to options outstanding on that date). Options may be granted under the Plan prior to the date of stockholder approval of the Plan (or extension of the Plan), but such options shall be granted subject to such approval. The Board may terminate or amend the Plan in any respect at any time, except that, without the approval of the stockholders (a) the total number of shares that may be issued under the Plan may not be increased (except by adjustment pursuant to Article 13); (b) the provisions of Article 3, regarding eligibility, may not be modified; (c) the provisions of Article 6, regarding the exercise price at which shares may be offered pursuant to options, may not be modified (except by adjustment pursuant to Article 13); (d) the expiration date of the Plan may not be extended; and (e) the benefits accruing to participants under the Plan may not be materially increased. No action of the Board or stockholders, however, may, without the consent of an optionee, substantially impair his rights under any option previously granted to him; and no amendment may cause any incentive stock options previously granted or to be granted under the Plan to cease to qualify as incentive stock options in accordance with the terms and conditions of the Plan.

-6-

Article 16 — Governmental Regulation

     The Plan and the grant and exercise of options thereunder, and the Company’s obligation to sell and deliver shares of the Company’s Common Stock under such options, shall be subject to all applicable laws (including tax laws), rules and regulations.

Article 17 — Withholding Taxes

     At any time when an optionee is required to pay to the Company an amount to be withheld under applicable income tax laws upon the exercise of a non-qualified stock option, the optionee may satisfy this obligation (to the extent of the minimum amount required to be withheld) in whole or in part by electing (the “Election”) to have the Company withhold from the distribution of shares of Common Stock, a number of shares of Common Stock having a value equal to the amount required to be withheld. The value of the shares to be withheld shall be based on the fair market value of the Common Stock on the Tax Date. Any fractional share amount left over after satisfying the withholding requirement must be paid to the optionee in cash. “Tax Date” means the date on which the amount of tax to be withheld with respect to the exercise of the non-qualified stock option is determined.

     Each such election must be made prior to the Tax Date. The Committee may disapprove the Election, may suspend or terminate the right to make an Election, or may provide with respect to any non-qualified option that the right to make an Election shall not apply to such option. An Election is irrevocable.

     If the optionee is subject to Section 16(b) of the Securities Exchange Act of 1934, an Election by such optionee is subject to the following additional restrictions:

     1. No Election shall be effective for a Tax Date which occurs within six months of the grant of the option, except that this limitation shall not apply in the event the death or disability of the optionee occurs prior to the expiration of the six-month period.

     2. The election must be made either six months prior to the Tax Date or must be made during a period beginning on the third business day following the date of release for publication of the Company’s quarterly or annual summary statements of sales and earnings and ending on the twelfth business day following such date.

A true copy.
	Attest: Date:
		Stanley D. Piekos

-7-

EX-5.1

Exhibit 5.1

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

November 15, 2005

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

Re: Brooks Automation, Inc.
Registration Statement on Form S-8 filed on November15, 2005

Ladies and Gentlemen:

This opinion is furnished to you in connection with the above-referenced registration statement (the “Registration Statement”), filed with the Securities and Exchange Commission under the Securities Act of 1933 (the “Act”), for the registration of 769,920 shares of common stock, par value $0.01 (the “Securities”), of Brooks Automation, Inc., a Delaware corporation (the “Company”), issuable upon exercise of options granted under: (i) the Helix Technology Corporation (“Helix”) 1996 Equity Incentive Plan, as Amended and Restated; (ii) the Amended and Restated Helix Stock Option Plan for Non-Employee Directors; and (iii) the Helix 1981 Employee Stock Option Plan, as amended.

I have acted as counsel for the Company in connection with the issuance of the Securities. For purposes of this opinion, I have examined and relied upon such documents, records, certificates and other instruments as I have deemed necessary. The opinions expressed below are limited to the Delaware General Corporation Law, including the applicable provisions of the Delaware Constitution and the reported cases interpreting those laws.

Based upon and subject to the foregoing, I am of the opinion that the Securities have been duly authorized, validly issued, fully paid and non-assessable. I hereby consent to your filing this opinion as an exhibit to the Registration Statement and to the use of my name therein. This opinion may be used only in connection with the offer and sale of the Securities while the Registration Statement is in effect.

Very truly yours,

/s/ Thomas S. Grilk, Esq.

Thomas S. Grilk, Esq.
Senior Vice-President and General Counsel

EX-23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We hereby consent to the incorporation by reference in this Registration Statement on Form S-8 of our report dated November 3, 2004, except for the second paragraph of Note 2 and Note 20, as to which the date is August 24, 2005 relating to the financial statements, which appears in Brooks Automation, Inc.’s Current Report on Form 8-K dated August 24, 2005.

/s/ PricewaterhouseCoopers LLP

Boston, Massachusetts
November 15, 2005