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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Form 10-K/A
Amendment No. 1
 (Mark One)
 þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the fiscal year ended March 31, 2006oro
    
    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
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ASYST TECHNOLOGIES, INC.
 Explanatory Note:
  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
  2




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SIGNATURES
  ASYST TECHNOLOGIES, INC.By:
    /s/  RICHARD H. JANNEYRichard H. JanneyInterim Chief Financial Officer  3




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##### 



EXHIBIT INDEX
 Incorporated by ReferenceExhibit
    
    
    
    
    
    
    
    
    
    
    
    
    
    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
 4




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##### 



Incorporated by ReferenceExhibit
    
    
    
    
    
    
    
    
    
    
    
    
    
    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
 5




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##### 



Incorporated by ReferenceExhibit
    
    
    
    
    
    
    
    
    
    
    
    
    
    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
    
    10/13/200631.1
    
    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).
    
    
    
    
    
    
    
    
    
    
    
    X32.1
    
    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 6