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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Form 10-K/A
 Amendment No. 2
 (Mark One)
 þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended March 31, 2006
 or
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 Commission file number 0-22430
 Asyst Technologies, Inc.
 (Exact name of registrant as specified in its charter)
 California
    
    94-2942251(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification No.)
 46897 Bayside Parkway, Fremont, California 94538  (Address of principal executive offices)
 (510) 661-5000  (Registrants telephone number, including area code)
 Securities registered pursuant to Section 12(b) of the Act:
 Title of Each Class
    
    Name of Each Exchange on Which RegisteredCommon Stock
    
    The NASDAQ Stock Market LLC(NASDAQ Global Market)
 Securities registered pursuant to Section 12(g) of the Act:
None
 o þ
 o þ
 þ o
 þ
  o þ o
 o þ




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##### Table of Contents



ASYST TECHNOLOGIES, INC.
 Explanatory Note:




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TABLE OF CONTENTS




|                                                     |      |   | 
|---------------------------------------------------- | ---- | - | 
|                                                     | Page
|PART IV                                              |      | 4 | 
|Item 15  Exhibits and Financial Statement Schedules |      | 4 | 
|SIGNATURES                                           |      | 5 | 
|EXHIBIT INDEX                                        |      |   | 
|EXHIBIT 23.1                                        
|EXHIBIT 31.1                                        
|EXHIBIT 31.2                                        
|EXHIBIT 32.1                                        





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PART IV
 
 Item 15  Exhibits and Financial Statement Schedules
 (a) The following documents are filed as part of this Annual Report on Form 10-K
 Financial Statements
  Financial Statement Schedule
  Exhibits
  4




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SIGNATURES
  ASYST TECHNOLOGIES, INC.By:
    /s/ RICHARD H. JANNEYRichard H. JanneyInterim Chief Financial Officer  5




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EXHIBIT INDEX
 Exhibit
    
    
    
    Incorporated by Reference
    
    
    
    FiledNumber
    
    Exhibit Description
    
    Form
    
    Ex. No.
    
    File No.
    
    Filing Date
    
    Herewith2.1
    
    Share Purchase Agreement dated as of June 22, 2006,between Shinko Electric Co.,
Ltd., Asyst Technologies, Inc. and Asyst Japan Inc. The schedules to the Share
Purchase Agreement are omitted but will be furnished to the Securities and Exchange
Commission supplementally upon request.
    
    8-K
    
    
    2.1
    
    
    000-22430
    
    7/20/20063.1
    
    Amended and Restated Articles of Incorporation of the Company.
    
    S-1
    
    
    3.1
    
    
    333-66184
    
    7/19/19933.2
    
    Bylaws of the Company.
    
    S-1
    
    
    3.2
    
    
    333-66184
    
    7/19/19933.3
    
    Certificate of Amendment of the Amended and Restated Articles of Incorporation,
filed September 24, 1999.
    
    10-Q
    
    
    3.2
    
    
    000-22430
    
    10/21/19993.4
    
    Certificate of Amendment of the Amended and Restated Articles of DEF Incorporation,
filed October 5, 2000.
    
    14A
    
    App.
    
    000-22430
    
    7/31/20004.1
    
    Rights Agreement among the Company and Bank of Boston, N.A., as Rights Agent, dated
June 25, 1998.
    
    8-K
    
    
    99.2
    
    
    000-22430
    
    6/29/19984.2
    
    Indenture dated as of July 3, 2001 between the Company, State Street Bank and Trust
Company of California, N.A., as trustee, including therein the forms of the notes.
    
    10-Q
    
    
    4.3
    
    
    000-22430
    
    8/14/20014.3
    
    Registration Rights Agreement dated as of July 3, 2001 between the Company and
Merrill Lynch & Co., Merrill Lynch, Pierce, Fenner & Smith, Incorporated, and ABN
Amro Rothschild LLC.
    
    10-Q
    
    
    4.4
    
    
    000-22430
    
    8/14/20014.4
    
    Amendment to Rights Agreement among the Company and Bank of Boston, N.A. as Rights
Agent, dated November 30, 2001.
    
    10-K
    
    
    4.5
    
    
    000-22430
    
    6/28/200210.1*
    
    Form of Indemnity Agreement entered into between the Company and certain directors.
    
    S-1
    
    
    10.1
    
    
    333-66184
    
    7/19/199310.2*
    
    Companys 1993 Stock Option Plan and related form of stock option agreement.
    
    S-1
    
    
    10.2
    
    
    333-88246
    
    2/13/199510.3*
    
    Companys 1993 Employee Stock Purchase Plan and related offering document.
    
    S-1
    
    
    10.3
    
    
    333-66184
    
    7/19/199310.4*
    
    Companys 1993 Non-Employee Directors Stock Option Plan and related offering
document.
    
    S-1
    
    
    10.4
    
    
    333-66184
    
    7/19/199310.5
    
    Hewlett-Packard SMIF License Agreement dated June 6, 1984.
    
    S-1
    
    
    10.5
    
    
    333-66184
    
    7/19/199310.6*
    
    Employment Agreement between the Company and Stephen S. Schwartz, Ph.D., dated
January 11, 2001.
    
    10-K
    
    
    10.27
    
    
    000-22430
    
    6/19/200110.7
    
    Agreement on Bank Transactions between Asyst Japan, Inc., or AJI, and Tokyo
Mitsubishi Bank dated March 13, 2001.
    
    10-Q
    
    
    10.28
    
    
    000-22430
    
    8/14/200110.8
    
    Share Purchase Agreement between Shinko Electric Co., Ltd. and Asyst Japan Inc.,
dated as of May 24, 2002.
    
    10-Q
    
    
    10.38
    
    
    000-22430
    
    11/12/200210.9
    
    Shareholders Agreement between Shinko Electric Co., Ltd. and Asyst Japan Inc.,
dated as of May 24, 2002.
    
    10-Q
    
    
    10.39
    
    
    000-22430
    
    11/12/2002




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Exhibit
    
    
    
    Incorporated by Reference
    
    
    
    FiledNumber
    
    Exhibit Description
    
    Form
    
    Ex. No.
    
    File No.
    
    Filing Date
    
    Herewith10.10
    
    Manufacturing Services and Supply Agreement
among the Company and Solectron Corporation
and its subsidiaries and affiliates, dated as
of September 5, 2002.
    
    10-Q
    
    
    10.40
    
    
    000-22430
    
    11/12/200210.11
    
    Amendment No. 1 to Shareholders Agreement
between Shinko Electric Co., Ltd. and Asyst
Japan Inc., dated as of October 16, 2002.
    
    10-Q
    
    
    10.43
    
    
    000-22430
    
    2/11/200310.12
    
    Patent Assignment and Cross-License and
Trademark License Agreement among the Company,
Entegris Cayman Ltd. And Entegris, Inc., dated
as of February 11, 2003.
    
    10-K/A
    
    
    10.44
    
    
    000-22430
    
    10/29/200310.13*
    
    Change-In-Control Agreement between the
Company and Stephen S Schwartz dated as of
October 20, 2003.
    
    10-Q
    
    
    10.47
    
    
    000-22430
    
    11/12/200310.14
    
    Amendment and Modification Agreement to
Manufacturing Services and Supply Agreement
among the Company and Solectron Corporation
and its subsidiaries and affiliates, effective
as of September 22, 2003.
    
    10-Q
    
    
    10.50
    
    
    000-22430
    
    2/10/200410.15*
    
    Form of Indemnity Agreement entered into
between the Company and certain executive
officers.
    
    10-K
    
    
    10.33
    
    
    000-22430
    
    6/10/200410.16*
    
    Form of Agreement to Arbitrate Disputes and
Claims entered into between the Company and
its executive officers.
    
    10-K
    
    
    10.37
    
    
    000-22430
    
    6/10/200410.17*
    
    Companys Compensation Program for
Non-employee Directors.
    
    10-K
    
    
    10.17
    
    
    000-22430
    
    10/13/200610.18*
    
    Companys Executive Deferred Compensation Plan.
    
    10-K
    
    
    10.39
    
    
    000-22430
    
    6/10/200410.19*
    
    Employment Agreement between the Company and
Stephen Debenham dated August 21, 2003.
    
    10-K
    
    
    10.40
    
    
    000-22430
    
    6/10/200410.20
    
    Amended and Restated Loan and Security
Agreement between the Company and Comerica
Bank, dated May 15, 2004.
    
    10-Q
    
    
    10.47
    
    
    000-22430
    
    8/5/200410.21*
    
    Forms of Stock Option Award Notice and Stock
Option Award Agreement entered into between
the Company and certain employees, directors,
and consultants (2003 Equity Incentive Plan).
    
    10-Q
    
    
    10.50
    
    
    000-22430
    
    12/30/200410.22*
    
    Forms of Restricted Stock Award Agreement for
restricted stock awarded to directors,
Restricted Stock Award Agreement for
restricted stock units awarded to directors,
Restricted Stock Award Agreement for
restricted stock awarded to employees, and
Restricted Stock Award Agreement for
restricted stock units awarded to employees.
    
    10-K
    
    
    10.22
    
    
    000-22430
    
    10/13/200610.23*
    
    Certificate of Amendment to Option Grants
dated August 18, 2004.
    
    10-Q
    
    
    10.52
    
    
    000-22430
    
    12/30/200410.24
    
    Companys 2001 Non-Officer Equity Plan.
    
    10-Q
    
    
    10.53
    
    
    000-22430
    
    12/30/200410.25*
    
    Employment Agreement between the Company and
Warren Kocmond, Jr., (corrected as of May 16,
2005).
    
    10-K
    
    
    10.52
    
    
    000-22430
    
    6/29/200510.26*
    
    Change-in-Control Agreement between the
Company and Robert J Nikl dated November 3,
2004.
    
    10-K
    
    
    10.53
    
    
    000-22430
    
    6/29/200510.27*
    
    Change-in-Control Agreement between the
Company and Anthony C. Bonora dated November
3, 2004.
    
    10-K
    
    
    10.54
    
    
    000-22430
    
    6/29/2005




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##### Table of Contents



Exhibit
    
    
    
    Incorporated by Reference
    
    
    
    FiledNumber
    
    Exhibit Description
    
    Form
    
    Ex. No.
    
    File No.
    
    Filing Date
    
    Herewith10.28
    
    Amendment No. 2 to Manufacturing Services and Supply Agreement among the Company
and Solectron Corporation and its subsidiaries and affiliates, effective February
17, 2005.
    
    10-K
    
    
    10.55
    
    
    000-22430
    
    6/29/200510.29
    
    Amendment No. 3 to Manufacturing Services and Supply Agreement among the Company
and Solectron Corporation and its subsidiaries and affiliates, effective June 10,
2005.
    
    10-K
    
    
    10.56
    
    
    000-22430
    
    6/29/200510.30*
    
    Summary of Executive Bonus Plan (revised 2006).
    
    10-K
    
    
    10.30
    
    
    000-22430
    
    10/13/200610.31
    
    Waiver and Amendment Number One to Amended and Restated Loan and Security Agreement
between the Company and Comerica Bank, dated June 27, 2005.
    
    10-K
    
    
    10.58
    
    
    000-22430
    
    6/29/200510.32*
    
    2003 Equity Incentive Plan as amended and approved by the Registrants shareholders
through August 23, 2005.
    
    8-K
    
    
    99.1
    
    
    000-22430
    
    8/29/200510.33*
    
    Employment Agreement dated as of August 29, 2005, between the Company and Alan S.
Lowe.
    
    10-Q
    
    
    10.60
    
    
    000-22430
    
    11/9/200510.34
    
    Amendment Number Two to Amended and Restated Loan and Security Agreement between
the Company and Comerica Bank, dated November 21, 2005.
    
    10-Q
    
    
    10.61
    
    
    000-22430
    
    2/6/200610.35
    
    Industrial Space Lease (Single Tenant Net) between the Company and JER Bayside, LLC
dated November 29, 2005.
    
    10-Q
    
    
    10.62
    
    
    000-22430
    
    2/6/200610.36*
    
    First Amendment dated December 16, 2005, to Change-in-Control Agreement dated
October 20, 2003, between the Company and Stephen S. Schwartz.
    
    8-K
    
    
    99.1
    
    
    000-22430
    
    12/16/200510.37
    
    Amendment No. 4 to Manufacturing Services and Supply Agreement among the Company
and Solectron Corporation and its subsidiaries and affiliates, effective August 1,
2005.
    
    10-K
    
    
    10.37
    
    
    000-22430
    
    10/13/200610.38
    
    Amendment No. 5 to Manufacturing Services and Supply Agreement among the Company
and Solectron Corporation and its subsidiaries and affiliates, effective March 20,
2006.
    
    10-K
    
    
    10.38
    
    
    000-22430
    
    10/13/200610.39*
    
    Separation Agreement and Release of All Claims between the Company and Warren C.
Kocmond, dated May 31, 2006.
    
    10-K
    
    
    10.39
    
    
    000-22430
    
    10/13/200610.40*
    
    Change-in-Control Agreement between the Company and Steve Debenham, dated May 22,
2006.
    
    10-K
    
    
    10.40
    
    
    000-22430
    
    10/13/200610.41*
    
    Change-in-Control Agreement between the Company and Alan S. Lowe, dated May 22,
2006.
    
    10-K
    
    
    10.41
    
    
    000-22430
    
    10/13/200610.42
    
    Credit Agreement among Asyst Technologies, Inc., Asyst Japan, Inc., Bank of
America, N.A., Banc of America Securities LLC, Keybank National Association, and
Comerica Bank dated as of June 22, 2006.
    
    10-K
    
    
    10.42
    
    
    000-22430
    
    10/13/200621.1
    
    Subsidiaries of Asyst Technologies, Inc.
    
    10-K
    
    
    21.1
    
    
    000-22430
    
    10/13/200623.1
    
    Consent of Independent Registered Public Accounting
Firm.
    
    
    
    
    
    
    
    
    
    
    
    X31.1
    
    Certification of the Chief Executive Officer of the Registrant required by SEC Rule
13a-14(a) (pursuant to Section 302 of the Sarbanes-Oxley Act of 2002).
    
    
    
    
    
    
    
    
    
    
    
    X31.2
    
    Certification of the Chief Financial Officer of the Registrant required by SEC Rule
13a-14(a) (pursuant to Section 302 of the Sarbanes-Oxley Act of 2002).
    
    
    
    
    
    
    
    
    
    
    
    X




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Exhibit
    
    
    
    Incorporated by Reference
    
    
    
    FiledNumber
    
    Exhibit Description
    
    Form
    
    Ex. No.
    
    File No.
    
    Filing Date
    
    Herewith32.1
    
    Combined Certification of the Chief Executive Officer and the Chief Financial
Officer of the Registrant required by SEC Rule 13a-14(b) (pursuant to Section 906
of the Sarbanes-Oxley Act of 2002).
    
    
    
    
    
    
    
    
    
    
    
    X
 
 *
    
    Indicates a management contract or compensatory plan or arrangement.
    
    Indicates English translation of original document.
    
    Indicates confidential treatment has been requested for portions of this document