##### Table of Contents



UNITED STATES SECURITIES AND
    EXCHANGE COMMISSION
 Washington, D.C.
    20549
  Form 10-K
  (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
    incorporation or organization)

(I.R.S. Employer
    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
  o þ
  Regulation S-K Form 10-K Form 10-K. þ
  Rule 12b-2
 o þ o
  Rule 12b-2 o þ




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##### 



ASYST
    TECHNOLOGIES, INC.
  TABLE OF
    CONTENTS
  
  Page No.PART IItem 1.

Business


2Item 1A.

Risk
    Factors


11Item 1B.

Unresolved Staff
    Comments


24Item 2.

Properties


24Item 3.

Legal
    Proceedings


24Item 4.

Submission of
    Matters to a Vote of Security  Holders


26PART IIItem 5.

Market for the
    Registrants Common Equity, Related Stockholder Matters and
    Issuer Purchases of Equity Securities


26Item 6.

Selected Financial
    Data


27Item 7.

Managements
    Discussion and Analysis of Financial  Condition and Results of
    Operations


29Item 7A.

Quantitative and
    Qualitative Disclosures About  Market Risk


50Item 8.

Financial
    Statements and Supplementary Data


51Item 9.

Changes in and
    Disagreements with Accountants on  Accounting and Financial
    Disclosure


98Item 9A.

Controls and
    Procedures


98Item 9B.

Other
    Information


104PART IIIItem 10.

Directors and
    Executive Officers of the Registrant


104Item 11.

Executive
    Compensation


108Item 12.

Security Ownership
    of Certain Beneficial Owners and Management and Related
    Stockholder Matters


114Item 13.

Certain
    Relationships and Related Transactions


118Item 14.

Principal
    Accounting Fees and Services


118PART IVItem 15.

Exhibits, Financial
    Statement Schedules


118Signatures


124EXHIBIT 10.17EXHIBIT 10.22EXHIBIT 10.30EXHIBIT 10.37EXHIBIT 10.38EXHIBIT 10.39EXHIBIT 10.40EXHIBIT 10.41EXHIBIT 10.42EXHIBIT 21.1EXHIBIT 23.1EXHIBIT 31.1EXHIBIT 31.2EXHIBIT 32.1




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PART I
    FORWARD LOOKING STATEMENTS



Except for the historical information contained herein, the
    following discussion includes forward-looking statements within
    the meaning of Section 27A of the Securities Act of 1933,
    and Section 21E of the Securities Exchange Act of 1934 that
    involve risks and uncertainties. We intend such forward-looking
    statements to be covered by the safe harbor provisions for
    forward-looking statements contained in the Private Securities
    Litigation Reform Act of 1995 and we are including this
    statement for purposes of complying with these safe harbor
    provisions. We have based these forward-looking statements on
    our current expectations and projections about future events.
    Our actual results could differ materially, as a result of
    certain factors including but not limited to those discussed in
    Risk Factors in this report and our other Securities
    and Exchange Commission (SEC) filings. These
    forward-looking statements are not guarantees of future
    performance and are subject to risks, uncertainties and
    assumptions, including those set forth in this section as well
    as those under the caption, Item 1A Risk
    Factors.



Words such as expect, anticipate,
    intend, plan, believe,
    estimate and variations of such words and similar
    expressions are intended to identify such forward-looking
    statements. Except as may be required by law, we do not intend
    to publicly update or revise any forward-looking statements,
    whether as a result of new information, future events or
    otherwise. In light of these risks, uncertainties and
    assumptions, the forward-looking events discussed in this report
    might not occur.



The following discussion should be read in conjunction with
    the audited condensed consolidated financial statements and
    related notes included in this report and our audited
    consolidated financial statements and related notes as of
    March 31, 2006, and for each of the three years in the
    period ended March 31, 2006 as filed in this report.
    Certain prior period amounts have been reclassified to conform
    to current period presentation.



Unless expressly stated or the context otherwise requires, the
    terms we, our, us,
    ATI, Asyst and the Company
    refer to Asyst Technologies, Inc. and its subsidiaries.



ASYST, the Asyst logo, Advan Tag, Domain Logix, Fastrack,
    Fluorotrack, IsoPort, Spartan and Versaport are registered
    trademarks of Asyst Technologies, Inc. or its subsidiaries, in
    the United States or in other countries. SMIF-Arms,
    SMIF-Indexer, SMIF-LPI, SMIF-LPO, SMIF-LPT, Plus, Inx, AdvanTag,
    SMART-Tag, SMART-Traveler, SMART-Comm, IsoPort, EIB and NexEDA
    are trademarks of Asyst Technologies, Inc. or its subsidiaries,
    in the United States or in other countries. Asyst Shinko is a
    trademark of Asyst Shinko, Inc. (ASI) or its
    subsidiaries, in the United States or in other countries. All
    other brands, products or service names are or may be trademarks
    or service marks of, and are used to identify products or
    services of, their respective owners.



EXPLANATORY
    NOTE



On June 9, 2006, the Companys Board of Directors
    appointed a special committee of three independent directors to
    conduct a formal investigation into past stock option grants and
    practices. The Special Committees investigation was
    completed on September 28, 2006, with the delivery of the
    Committees final report on that date. The Special
    Committee found instances wherein incorrect measurement dates
    were used to account for certain option grants.



Based on the results of the Special Committees
    investigation, the Company recorded stock-based compensation
    charges, and additional payroll taxes, with respect to its
    employee stock option grants for which the measurement dates
    were found to be in error. Accordingly, the Company restated the
    results of fiscal years 2005 and 2004, to record a net charge of
    approximately $0.2 million or $0.00 per share in
    fiscal 2005 and a net benefit of $0.8 million or
    $0.02 per share in fiscal 2004. Additionally, the Company
    recorded a net charge of $19.5 million to its accumulated
    deficit as of April 1, 2003 for cumulative charges relating
    to fiscal years prior to fiscal 2004. For more information on
    these matters, please refer to the following:



Part I  Item 1A  Risk Factors;



Part I  Item 3  Legal
    Proceedings;

1




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Item 1 
    Business  Overview
  work-in-process.
  
    The use of larger diameter silicon wafers, which require
    automated handling because of ergonomic issues and increased
    yield risk.
    The use of larger size glass panels for the manufacturing of
    FPDs, which require automated handling because of the extreme
    bulk and weight of the panels.
    Continuing decreases in semiconductor device line widths, which
    require higher levels of cleanliness in the manufacturing
    process.
    Increasingly complex semiconductor devices, which require more
    process steps and thus greater transportation and tool loading
    capabilities.
    Continuing customer requirements for enhanced manufacturing
    control, productivity and return on capital.    Acquisition
    and Related Debt Financing Facility
      3 4
 2




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Fiscal
    Year-end Dates
    Industry
    Background
    work-in-process work-in-process
    work-in-process
   3




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The Asyst
    Solution
    Increased Manufacturing Productivity.
  Higher Yields. work-in-process
    Strategy
    and Business Developments
    Further Penetrate the Markets for Semiconductor and FPD
    AMHS.
  Increase Penetration of New Tool and Fab Automation
    Products.
 4




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Focus on Supply Chain Excellence.
  Increase customer satisfaction.
  Products
  Tool
    Automation Components
    Loadports
    Substrate-Handling
    Robotics
    Systems
    EFEMs
   5




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work-in-process set-up
    Sorters
    AMHS for
    Semiconductor Manufacturing
  bay-to-bay
  Wafer Stockers.
  OHT.
  OHS.
  AGV.
  Rail Guided Vehicle (RGV).
  AMHS for
    FPD Manufacturing
  LCD Stocker. work-in-progress
 6




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LCD AGVs.
  Connectivity
    Solutions
  Auto-ID
    Systems
  work-in-process
  Software
    Customers
      Sales and
    Marketing
   7




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Research
    and Development
      Manufacturing
  and/or
  U.S.-based
  Competition
     8




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Intellectual
    Property
  and/or
     9




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Backlog
    Employees
    Financial
    Information by Business Segment and Geographic Data
    Environmental
    Compliance
    Additional
    Information and Governance Matters
      Form 10-K, Form 10-Q, Form 8-K,
   10




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##### Table of Contents



Form 10-K.
  Form 8-K. Form 8-K Form 8-K
   Item 1A 
    Risk Factors  We
    have a history of significant losses.
    We
    face significant pending and potential risks in connection with
    our outstanding indebtedness; if we are not able to resolve
    existing uncertainties and restructure portions of this debt on
    a timely basis on desired terms in the future, our ability to
    discharge our obligations under this indebtedness, liquidity and
    business may be materially harmed.
    
    Under a senior secured credit agreement entered into in June
    2006 with Bank of America, N.A., as lender and administrative
    agent and other lenders, we borrowed an aggregate amount of
    approximately $81.5 million to fund the purchase of ASI
    shares from Shinko on July 14, 2006, as described under
    Item 1  Business, Share Purchase
    Agreement, and issued a letter of credit in favor of
    Shinko for approximately $11 million related to the equity
    option on Shinkos remaining 4.9% ASI share ownership. This
    credit agreement provides a $115 million senior secured
    credit facility consisting of a $90 million revolving
    credit facility, including a $20 million sub-limit for
    letters of credit and $10 million sub-limit for swing-line
    loans, and a $25 million term loan facility. The credit
    agreement will terminate and all amounts outstanding will be due
    in three years after July 14, 2006, provided that
    Asysts outstanding
    53/4%
    convertible subordinated notes due July 3, 2008, are
    redeemed or repurchased, or the maturity of the notes extended,
    on terms reasonably satisfactory to the administrative agent on
    or before March 31, 2008; otherwise, amounts outstanding
    under the credit agreement will be due on March 31, 2008.
    We have approximately $86.3 million outstanding under our
    53/4% convertible
    subordinated notes privately issued in July 2001. These notes
    are convertible, at the option of the holder, at any time on or
    prior to maturity into shares of our common stock at a
    conversion price of $15.18 per share. We are required to
    pay interest on these convertible notes on January 3 and
    July 3 of each year. These notes mature July 3, 2008
    and are redeemable at our option.  
    In a letter delivered to us and dated August 16, 2006, the
    trustee under the indenture relating to these notes asserted
    that Asyst is in default under the notes indenture because
    of the previously announced delays in 11




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filing with the SEC and the trustee this report on
    Form 10-K
    and in filing with the SEC our
    Form 10-Q
    for the fiscal quarter ended June 30, 2006. The letter
    stated that this asserted default was not an Event of
    Default under the indenture if the Company cures the
    default within 60 days after receipt of the notice, or if
    the default is waived by the holders of a majority in aggregate
    principal amount of the notes outstanding.  
    If an Event of Default were to occur, and is continuing under
    the indenture, the trustee or the holders of at least 25% in
    aggregate principal amount of the notes at the time outstanding
    may accelerate maturity of the notes.
    Asyst does not agree with the trustees assertion that the
    delays in filing of the annual and quarterly reports constitutes
    a default under its indenture. Nonetheless, in conjunction with
    the filing of this report on
    Form 10-K,
    we intend to file with the SEC our report on
    Form 10-Q
    for the fiscal quarter ended June 30, 2006. Upon completion
    of those filings, we intend to deliver to the trustee copies of
    the reports on
    Forms 10-K
    and 10-Q,
    and that delivery will cure any purported defaults under the
    indenture and asserted by the trustee in its letter referenced
    above.  
    At March 31, 2006, ASI had five revolving lines of credit
    with Japanese banks. These lines allow aggregate borrowing of up
    to 7 billion Japanese Yen, or approximately
    $60 million at the exchange rate as of March 31, 2006.
    As of March 31, 2006, the amount available under these
    lines of credit was 7 billion Japanese Yen or approximately
    $60 million at the exchange rate as of March 31, 2006.
    Comerica Bank has agreed to continue to maintain a letter of
    credit in the amount of $750,000 in favor of the landlord under
    our current headquarters lease in Fremont, California, on an
    unsecured basis, notwithstanding the previously reported
    termination of the Amended and Restated Loan and Security
    Agreement dated as of May 15, 2004, between Asyst and
    Comerica Bank (which termination became effective with the
    borrowing described above under the senior secured credit
    facility). There were no amounts outstanding for borrowed money
    under the Comerica Bank line of credit that otherwise was
    scheduled to expire on July 30, 2007.  and/or
  and/or
  and/or
 12




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13




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We
    face additional risks and costs as a result of the delayed
    filing of our SEC reports described below and the time, cost and
    outcome of our Special Committee investigation into past stock
    option grants and practices.
  Form 10-K, Form 10-Q
               14




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Form 10-K Form 10-Q Form 10-K Form 10-Q
    In re Asyst Technologies, Inc. Derivative
    Litigation Forlenzo v. Schwartz, et al
    Form 10-Q Form S-3 Form S-3.
 15




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If we
    continue to fail to achieve and maintain effective disclosure
    controls and procedures and internal control over financial
    reporting on a consolidated basis, our stock price and investor
    confidence in our Company could be materially and adversely
    affected.
      Form 10-K
    If we
    fail to manage effectively our ASI subsidiary, our sales and
    profitability of AMHS could be adversely affected and the sales
    mix between AMHS and our other products could affect our overall
    financial performance.
      percentage-of-completion
   16




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If we
    are unable to increase our sales of AMHS to FPD manufacturers,
    or if the FPD industry enters a cyclical downturn, our growth
    prospects could be negatively affected.
  ASI sells AMHS to FPD manufacturers.
    Our
    gross margins on 300mm products may be lower, which could
    adversely affect our ability to remain profitable.
    Most
    of our Fab Automation Product manufacturing is outsourced and we
    rely on a single contract manufacturer for much of this
    manufacturing, which could disrupt the availability of our Fab
    Automation Products and adversely affect our gross
    margins.
     17




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Shortages
    of components necessary for product assembly by Solectron or us
    can delay shipments to our customers and can lead to increased
    costs, which may negatively impact our financial
    results.
    We may
    have additional tax liabilities that could be materially higher
    than we expect.
      Because
    we do not have long-term contracts with our customers, our
    customers may cease purchasing our products at any
    time.
    
    our customers can cease purchasing our products at any time,
    without penalty; 18




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
    our customers are free to purchase products from our competitors;
    we are exposed to competitive price pressure on each order;
    our customers are not required to make minimum
    purchases; and
    our customers may reschedule or cancel existing orders, and we
    may not be able to recover the costs we have incurred to
    manufacture that product from the customer.    We
    depend on large purchases from a few significant customers, and
    any loss, cancellation, reduction or delay in purchases by, or
    failure to collect receivables from these customers could harm
    our business.
    If we
    are unable to develop and introduce new products and
    technologies in a timely manner, our business could be
    negatively affected.
    We may
    be unable to protect our intellectual property rights and we may
    become involved in litigation concerning the intellectual
    property rights of others.
   19




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We may
    not be able to integrate efficiently the operations of our
    acquisitions, and may incur substantial losses in the
    divestiture of assets or operations.
    As our
    quarterly and yearly operating results are subject to
    variability, comparisons between periods may not be meaningful;
    this variability in our results could cause our stock price to
    decline.
    
    general trends in the overall economy, electronics industry and
    semiconductor and FPD manufacturing industries;
    fluctuations in the semiconductor and FPD equipment markets;
    changes in customer buying patterns;
    the degree of competition we face;
    pricing pressures causing lower gross margins or lost orders; 20




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
    the size, timing and product mix of customer orders;
    lost sales due to any failure in the outsourcing of our
    manufacturing;
    the availability of key components;
    the timing of product shipment and acceptance, which are factors
    in determining when we recognize revenue; and
    the timely introduction and acceptance of new products.  quarter-to-quarter year-to-year period-to-period
  We
    face significant economic and regulatory risks because a
    majority of our net sales are derived from outside the United
    States.
    
    exposure to currency fluctuations;
    the imposition of governmental controls;
    the laws of certain foreign countries may not protect our
    intellectual property to the same extent as do the laws of the
    United States;
    the need to comply with a wide variety of foreign and
    U.S. export laws;
    political and economic instability;
    terrorism and
    anti-American
    sentiment;
    trade restrictions;
    slowing economic growth and availability of investment capital
    and credit;
    changes in tariffs and taxes;
    longer product acceptance and payment cycles;
    the greater difficulty in administering business
    overseas; and
    inability to enforce payment obligations or recourse to legal
    protections accorded creditors to the same extent within the U.S.     21




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Our
    current and planned operations may strain our resources and
    increase our operating expenses.
      We
    have continued to experience unexpected turnover in our finance
    department, and this has had an adverse impact on our business;
    if we lose any of our key personnel or are unable to attract,
    train or retain qualified personnel, our business would be
    further harmed.
    Form 10-K Form 10-Q
   22




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Risks
    Related to our Industry
  The
    semiconductor manufacturing equipment industry is highly
    cyclical and is affected by recurring downturns in the
    semiconductor industry, and these cycles can harm our operating
    results.
        We may
    not effectively compete in a highly competitive semiconductor
    manufacturing equipment industry.
       23




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Item 1B 
    Unresolved Staff Comments   Item 2 
    Properties    SquareFootageLocation

Functions

(Approximate)

Lease Expiration

Facilities by SegmentsFremont, California

Corporate headquarters


95,000


March 2013

Fab Automation/AMHSFremont, California

Repair and maintenance


35,000


February 2008

Fab Automation/AMHSAndover, Massachusetts

Sales and support


5,000


April 2009

Fab AutomationRichardson, Texas

Sales and support


2,000


May 2009

Fab AutomationAustin, Texas

Sales and support, R&D


3,000


June 2008

Fab AutomationNagoya, Japan

Administration, manufacturing,
    R&D


65,000


Owned

Fab Automation/AMHSNagoya, Japan

Administration, manufacturing


7,000


December 2008

Fab AutomationNagoya, Japan

Warehouse


7,000


March 2008

Fab AutomationHsin-Chu City, Taiwan

Administration, sales and support


7,000


May 2007

Fab Automation/AMHSGenting, Singapore

Sales and support


2,000


September 2008

Fab AutomationIse, Japan

Administration, manufacturing,
    R&D


176,000


June 2011

AMHSTokyo, Japan

Sales and support


4,000


May 2008

AMHS    Item 3 
    Legal Proceedings     24




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In re Asyst
    Technologies, Inc. Derivative Litigation Forlenzo v. Schwartz, et al et. seq. Rule 10b-5 Rule 14a-9
   25




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Item 4 
    Submission of Matters to a Vote of Security
    Holders   PART II  Item 5 
    Market
    for Registrants Common Equity, Related Stockholder Matters
    and Issuer Purchases of Equity Securities    Form 10-K
  Form 10-Q
    Form 8-K
  
    On or before September 27, 2006, the Company submits
    supplemental information outlined in the letter concerning the
    previously announced Special Committee investigation into stock
    option grants and practices; and
    On or before November 30, 2006, the Company files its
    Form 10-K
    for the fiscal year ended March 31, 2006, its
    Form 10-Q
    for the quarter ended June 30, 2006, and all required
    restatements (if any).    Price
    Range of Common Stock
    High


LowFiscal year ended March 31,
    2005First quarter

$
10.51


$
6.30Second quarter

$
10.45


$
4.15Third quarter

$
5.68


$
3.68Fourth quarter

$
5.34


$
3.93Fiscal year ended March 31,
    2006First quarter

$
4.89


$
3.12Second quarter

$
5.49


$
4.41Third quarter

$
6.53


$
3.84Fourth quarter

$
11.20


$
5.55  26




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Approximate
    Number of Equity Security Holders
    Dividends
    Issuer
    Purchases of Equity Securities
   Item 6 
    Selected Financial Data  Fiscal
    Year-end Dates
    Selected
    Consolidated Financial Data
      March 31,2006


2005


2004


2003


2002(As restated)


(As restated)


(As restated)


(As restated)(in thousands)Consolidated Balance Sheet
    DataCash and cash equivalents and
    short-term investments

$
109,926


$
101,180


$
117,860


$
96,214


$
79,577Total assets


415,294



483,774



472,864



395,225



352,160Long-term debt and capital leases,
    net of current portion


87,168



88,750



91,074



114,812



90,331Shareholders equity


87,679



89,717



102,252



62,622



167,185   27




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Fiscal Year Ended March 31,2006


2005


2004


2003


2002(As restated)


(As restated)


(As restated)


(As restated)(In thousands, except per share data)Consolidated Statements of
    Operations Data:Net sales

$
459,221


$
612,987


$
301,642


$
259,495


$
183,234Gross profit


161,246



122,215



53,370



74,637



40,463In-process research and
    development of acquired businesses














7,832



2,000Income (loss) from operations


32,286



(17,829
)


(86,489
)


(86,581
)


(136,123
)Gain on sale of wafer and reticle
    carrier product line














28,420



Loss from continuing operations
    before discontinued operations and cumulative effect of a change
    in accounting principle


(104
)


(17,743
)


(82,616
)


(122,607
)


(99,937
)Discontinued operations, net of
    income tax














(21,096
)


(51,403
)Net loss


(104
)


(17,743
)


(82,616
)


(143,703
)


(151,340
)Net loss per share from continuing
    operations before discontinued operations and cumulative effect
    accounting of a change in principle:Basic and diluted

$
(0.00
)

$
(0.37
)

$
(1.98
)

$
(3.27
)

$
(2.85
)Discontinued operations, net of
    income taxes

$



$



$



$
(0.56
)

$
(1.45
)Shares used in earnings per share
    calculation:Basic and diluted


47,972



47,441



41,805



37,489



35,373            28




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Form 10-K
 Item 7 
    Managements Discussion and Analysis of Financial
    Condition and Results of Operations  The following discussion of our financial condition and
    results of operations should be read in conjunction with our
    consolidated financial statements and the related notes included
    elsewhere in this Annual Report on
    Form 10-K.
    This discussion contains forward-looking statements, which
    involve risk and uncertainties. Our actual results could differ
    materially from those anticipated in the forward looking
    statements as a result of certain factors, including but not
    limited to those discussed in Item 1A Risk
    Factors and elsewhere in this Annual Report.
  Our Past
    Stock Option Grant Practices, and Need to Restate our Financial
    Statements
  Form 10-K,
         29




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Cost of
    Restatement and Legal Activities
  Form 10-K Form 10-Q
  In re Asyst
    Technologies, Inc. Derivative Litigation Forlenzo v. Schwartz, et al
    Overview
         31




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and/or
    Internal
    Control Matters
  Form 10-K
  If we
    continue to fail to achieve and maintain effective disclosure
    controls and procedures and internal control over financial
    reporting on a consolidated basis, our stock price and investor
    confidence in our Company could be materially and adversely
    affected.
  Critical
    Accounting Policies and Estimates
  General
      Revenue
    Recognition
   32




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and/or
  Accounting for Performance of
    Construction-Type and Certain Production-Type Contracts. percentage-of-completion
    SOP 97-2, Software Revenue Recognition. percentage-of-completion
  Allowance
    for Doubtful Accounts
    Inventory
    Reserves
  work-in-process,
 33




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Goodwill
    and Other Intangible Assets
    Warranty
    Reserve
    Accounting
    for Income Taxes
      Impairment
    of Long-Lived Assets
   34




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##### Table of Contents



Results
    of Operations
  Comparison
    of Sales, Gross Profit, Expenses, Interest & Other, and
    Taxes
    Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)NET SALES


100.0
%


100.0
%


100.0
%COST OF SALES


64.9
%


80.1
%


82.3
%GROSS PROFIT


35.1
%


19.9
%


17.7
%OPERATING EXPENSES:Research and development


6.1
%


5.7
%


12.0
%Selling, general and administrative


18.4
%


12.7
%


23.3
%Amortization of acquired
    intangible assets


3.6
%


3.3
%


6.7
%Restructuring and other charges
    (credits)


(0.0
)%


0.3
%


2.2
%Asset impairment charges


0.0
%


0.8
%


2.2
%Total operating expenses


28.1
%


22.8
%


46.4
%INCOME (LOSS) FROM OPERATIONS


7.0
%


(2.9
)%


(28.7
)%INTEREST AND OTHER INCOME
    (EXPENSE), NET:Interest income


0.6
%


0.3
%


0.3
%Interest expense


(1.5
)%


(1.1
)%


(2.4
)%Other income (expense), net


1.1
%


0.7
%


(0.1
)%Interest and other (expense), net


0.2
%


(0.1
)%


(2.2
)%INCOME (LOSS) BEFORE (PROVISION
    FOR) BENEFIT FROM INCOME TAXES AND MINORITY INTEREST


7.2
%


(3.0
)%


(30.9
)%BENEFIT FROM (PROVISION FOR)
    INCOME TAXES


(4.1
)%


0.3
%


2.0
%MINORITY INTEREST


(3.1
)%


(0.2
)%


1.5
%NET LOSS


(0.0
)%


(2.9
)%


(27.4
)%  35




---



##### Table of Contents



Fiscal Year Ended March 31,2005


20042006


(As reported)


(Adjustments)


(As restated)


(As reported)


(Adjustments)


(As restated)AMHS:Net sales

$
294,483


$
380,596


$



$
380,596


$
168,510


$



$
168,510Cost of Sales


196,571



333,956







333,956



145,636







145,636Gross Profit

$
97,912


$
46,640


$



$
46,640


$
22,874


$



$
22,874Income (loss) from operations

$
47,782


$
844


$



$
844


$
(19,245
)

$



$
(19,245
)Fab Automation
    Products:Net sales

$
164,738


$
232,391


$



$
232,391


$
133,132


$



$
133,132Cost of Sales


101,404



156,774



42



156,816



102,817



(181
)


102,636Gross Profit

$
63,334


$
75,617


$
(42
)

$
75,575


$
30,315


$
181


$
30,496Income (loss) from operations

$
(15,496
)

$
(18,472
)

$
(201
)

$
(18,673
)

$
(68,077
)

$
833


$
(67,244
)Consolidated:Net sales

$
459,221


$
612,987


$



$
612,987


$
301,642


$



$
301,642Cost of Sales


297,975



490,730



42



490,772



248,453



(181
)


248,272Gross Profit

$
161,246


$
122,257


$
(42
)

$
122,215


$
53,189


$
181


$
53,370Income (loss) from operations

$
32,286


$
(17,628
)

$
(201
)

$
(17,829
)

$
(87,322
)

$
833


$
(86,489
)   Net
    Sales
       36




---



##### Table of Contents



Fiscal Year Ended March 31,2006


2005


2004United States

$
87,266


$
112,923


$
63,863Japan


183,079



146,752



83,778Taiwan


109,174



230,334



46,211Korea


21,123



30,240



45,785Other Asia/Pacific


27,336



70,879



41,381Europe


31,243



21,859



20,624Total

$
459,221


$
612,987


$
301,642     Gross
    Profit
      quarter-over-quarter
 37




---



##### Table of Contents



Research
    and Development
  Fiscal Year Ended March 31,20052006


(As reported)


(Adjustments)


(As restated)


Change(In thousands, except percentage)Research and development

$
27,913


$
34,747


$
62


$
34,809


$
(6,896
)Percentage of total net sales


6.1
%


5.7
%






5.7
%   2005


2004(As restated)


(As reported)


(Adjustments)


(As restated)


ChangeResearch and development

$
34,809


$
36,376


$
(443
)

$
35,933


$
(1,124
)Percentage of total net sales


5.7
%


12.0
%






11.9
%     Selling,
    General and Administrative
  Fiscal Year Ended March 31,20052006


(As reported)


(Adjustments)


(As restated)


Change(In thousands, except percentage)Selling, General and Administrative

$
84,503


$
78,247


$
97


$
78,344


$
6,159Percentage of total net sales


18.4
%


12.7
%






12.7
%   2005


2004(As restated)


(As reported)


(Adjustments)


(As restated)


ChangeSelling, General and Administrative

$
78,344


$
70,541


$
(209
)

$
70,332


$
8,012Percentage of total net sales


12.7
%


23.4
%






23.3
%     Form 10-Q
 38




---



##### Table of Contents



Amortization
    of Acquired Intangible Assets
  Fiscal Year Ended March 31,2006


2005


Change

2005


2004


Change(In thousands, except percentage)Amortization of acquired
    intangible assets

$
16,590


$
20,436


$(3,846)

$
20,436


$
20,160


$276Percentage of total net sales


3.6
%


3.3
%




3.3
%


6.7
%     Restructuring
    and Other Charges (Credits)
    Severance and


Excess


Fixed AssetsBenefits


Facilities


Impairment


TotalBalance, March 31, 2003

$
291


$
3,617


$
192


$
4,100Additional (reduction in) accruals


5,460



1,075



46



6,581Non-cash related utilization


70



(444
)


(205
)


(579
)Amounts paid in cash


(5,757
)


(2,058
)


(33
)


(7,848
)Balance, March 31, 2004


64



2,190







2,254Additional (reduction in) accruals


1,803



7







1,810Amounts paid in cash


(1,803
)


(1,390
)






(3,193
)Foreign currency translation
    adjustment


3



9







12Balance, March 31, 2005


67



816







883Additional (reduction in) accruals


(7
)


(39
)






(46
)Non-cash related utilization


(60
)


(96
)






(156
)Amounts paid in cash






(573
)






(573
)Foreign currency translation
    adjustment






(3
)






(3
)Balance, March 31, 2006

$



$
105


$



$
105        39




---



##### Table of Contents



Asset
    Impairment Charges
    Fiscal Year Ended March 31,2006

2005

2004Land and building impairment

$



$
4,645


$
6,853   held-for-sale
  held-and-used.
    Interest
    and Other Income (Expense), Net
  Fiscal Year Ended March 31,


Fiscal Year Ended March 31,2006


2005


Change


2005


2004


Change(In thousands)Interest income

$
2,527


$
1,722


$
805


$
1,722


$
815


$
907Interest expense


(6,746
)


(6,747
)


1



(6,747
)


(7,213
)


466Other income (expense), net


5,172



4,296



876



4,296



(237
)


4,533Total, net

$
953


$
(729
)

$
1,682


$
(729
)

$
(6,635
)

$
5,906     Provision
    for (Benefit from) Income Taxes
  Fiscal Year Ended March 31,


Fiscal Year Ended March 31,2006


2005


Change


2005


2004


Change(In thousands, except percentage)Provision for (benefit from)
    income taxes

$
18,746


$
(1,916
)

$
20,662


$
(1,916
)

$
(6,150
)

$
4,234Percentage of total net sales


4.1
%


(0.3
)%






(0.3
)%


(2.0
)%    40




---



##### Table of Contents



Minority
    Interest
    Related
    Party Transactions
      Fiscal Year Ended March 31,2006


2005Accounts payable due to Shinko

$
13,406


$
39,221Accrued liabilities due to Shinko

$
59


$
450Accounts receivable from MECS Korea

$
90


$
100Accounts payable due to MECS Korea

$
3


$
21Accrued liabilities due to MECS
    Korea

$
81


$
     Fiscal Year Ended March 31,2006


2005


2004Material and service purchases
    from Shinko

$
57,043


$
96,097


$
42,511Material and service purchases
    from MECS Korea

$
3


$
414


$
2Sales to MECS Korea

$
568


$
378


$
138  41




---



##### Table of Contents



Recent
    Accounting Pronouncements
  Inventory Costs  an Amendment of ARB No. 43,
    Chapter 4
  Exchange of Nonmonetary Assets  an amendment of
    APB Opinion No. 29
          Accounting Changes and Error Corrections: a Replacement of
    Accounting Principles Board Opinion No. 20
    (APB 20) and FASB Statement No 3
 42




---



##### Table of Contents



No. FAS 13-1, Accounting for Rental Costs Incurred during a Construction
    Period 13-1). 13-1 13-1
  FAS 115-1 FAS 124-1, The Meaning of
    Other-Than-Temporary
    Impairment and Its Application to Certain Investments, other-than-temporary other-than-temporary Not-for-Profit
  Accounting for Uncertainty in Income Taxes: An Interpretation
    of FASB Statement No. 109
  No. 06-2, (EITF 06-2). EITF 06-2 EITF 06-2 EITF 06-02
    Fair Value Measurements
 43




---



##### Table of Contents



Accounting for Defined Benefit Pension and Other
    Postretirement Plans  an amendment of FASB Statements
    No. 87, 88, 106, and 132(R not-for-profit
  Liquidity
    and Capital Resources
        Fiscal Year Ended March 31,2006


2005


2004Net cash provided by (used in)
    operating activities

$
43.7


$
(17.7
)

$
(67.8
)Net cash provided by (used in)
    investing activities

$
22.1


$
(7.3
)

$
(23.8
)Net cash provided by (used in)
    financing activities

$
(24.0
)

$
4.2


$
87.2   Cash
    flows from operating activities.
    Net loss

$
(0.1
)Depreciation and amortization


23.3Allowance for doubtful accounts


6.8Minority interest in net income of
    consolidated subsidiary


14.6Other non-cash charges


(2.2
)Decrease in accounts receivable


29.1Increase in inventories


(2.0
)Decrease in prepaid expenses and
    other assets


8.1Decrease in accounts payable,
    accrued liabilities and deferred margin


(33.9
)Net cash provided by operating
    activities

$
43.7    44




---



##### Table of Contents



Cash
    flows from investing activities.
        Cash
    flows from financing activities.
   45




---



##### Table of Contents



3 4
  Notice of
    default relating to Convertible Subordinated Notes.
  3 4 Form 10-K Form 10-Q
    Form 10-K Form 10-Q Form 10-K Form 10-Q,
  Acquisition
    and related debt financing facility.
     46




---



##### Table of Contents



Other
    debt financing arrangements.
             47




---



##### Table of Contents



Other
    liquidity considerations.
  and/or and/or
    NASDAQ
    Delisting Proceedings
  Form 10-K Form 12b-25 Form 10-K
  
    On or before September 27, 2006, the Company submits
    supplemental information outlined in the letter concerning the
    previously announced Special Committee inquiry into stock option
    grants and practices; and
    On or before November 30, 2006, the Company files its
    Form 10-K
    for the fiscal year ended March 31, 2006, its
    Form 10-Q
    for the quarter ended June 30, 2006, and all required
    restatements (if any).   48




---



##### Table of Contents



Form 10-K Form S-3 Form S-3 Form S-1.
  Overview  Internal Control
    Matters Form 10-K
  Off-Balance
    Sheet Arrangements
    Contractual
    Obligations
    Payments Due by PeriodLess Than








More ThanTotal


1 Year


1-3 Years


3-5 Years


5 YearsShort-term loans and notes payable

$
1,443


$
1,443


$



$



$
Long-term debt, including interest


88,012



1,153



86,859







Capital lease obligations,
    including interest


541



231



310







Operating lease obligations


13,753



3,292



4,774



2,890



2,797Purchase obligations


13,606



13,606











Defined benefit pension plan
    obligations


14,066



893



4,261



4,657



4,255Total

$
131,421


$
20,618


$
96,204


$
7,547


$
7,052      49




---



##### Table of Contents



Item 7A 
    Quantitative and Qualitative Disclosures About Market
    Risk  Interest Rate Risk.
      Remaining

Principal


Weighted AverageMaturities

Amount


Interest Rate(In thousands)CASH EQUIVALENTS:Institutional money market funds

within 1 year

$
19,756


4.14%  4.64%Commercial paper

within 1 year


2,993


4.52%  4.59%Total cash equivalents



$
22,749SHORT-TERM
    INVESTMENTS:Auction rate securities

within 39 years

$
8,300


4.5%  4.86%Corporate debt securities

within 1 year


6,005


3.3%  3.71%Federal agency notes

within 1 year


999


2.73%Total short-term investments



$
15,304     Foreign Currency Exchange Risk.
  Strengthening in Japanese

No change inYen of X Percent

Japanese Yen10%

5%

Exchange RateNet income (loss) for the fiscal
    year ended March 31, 2006

$
3,926


$
1,805


$
(104
)  50




---



##### Table of Contents



Item 8 
    Financial Statements and Supplementary Data  Consolidated
    Financial Statements
  PageConsolidated
    Balance Sheets


52Consolidated
    Statements of Operations


53Consolidated
    Statements of Shareholders Equity


54Consolidated
    Statements of Cash Flows


55Notes to
    Consolidated Financial Statements


56Report of
    Independent Registered Public Accounting Firm


94   Financial
    Statement Schedule
     51




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  CONSOLIDATED
    BALANCE SHEETS
  March 31,2006


2005(As restated)(In thousands, exceptshare data)ASSETSCURRENT ASSETS:Cash and cash equivalents

$
94,622


$
55,094Short-term investments


15,304



46,086Accounts receivable, net


141,453



189,943Inventories


33,219



33,515Prepaid expenses and other current
    assets


26,831



33,971Total current assets


311,429



358,609Property and equipment, net


23,108



15,458Goodwill


58,840



64,014Intangible assets, net


19,334



40,898Other assets


2,583



4,795$
415,294


$
483,774LIABILITIES, MINORITY INTEREST
    AND SHAREHOLDERS EQUITYCURRENT LIABILITIES:Short-term loans and notes payable

$
1,443


$
20,563Current portion of long-term debt
    and capital leases


1,368



2,757Accounts payable


75,376



83,913Accounts payable-related parties


13,409



39,242Accrued and other liabilities


62,902



70,645Deferred margin


5,335



6,013Total current liabilities


159,833



223,133LONG-TERM LIABILITIESLong-term debt and capital leases,
    net of current portion


87,168



88,750Deferred tax liability


3,119



8,548Other long-term liabilities


10,974



9,771Total long-term liabilities


101,261



107,069COMMITMENTS AND CONTINGENCIES (see
    Notes 13 and 15)MINORITY INTEREST


66,521



63,855SHAREHOLDERS EQUITYCommon stock, no par value:Authorized shares 
    300,000,000Outstanding shares 
    48,462,235 and 47,779,539 shares at March 31, 2006 and
    2005, respectively


473,422



469,201Deferred stock-based compensation


(1,319
)


(1,879
)Accumulated deficit


(385,178
)


(385,074
)Accumulated other comprehensive
    income


754



7,469Total shareholders equity


87,679



89,717Total liabilities, minority
    interest and shareholders equity

$
415,294


$
483,774    52




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF OPERATIONS
  Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)(In thousands, except per share data)NET SALES

$
459,221


$
612,987


$
301,642COST OF SALES


297,975



490,772



248,272GROSS PROFIT


161,246



122,215



53,370OPERATING EXPENSES:Research and development


27,913



34,809



35,933Selling, general and administrative


84,503



78,344



70,332Amortization of acquired
    intangible assets


16,590



20,436



20,160Restructuring and other charges
    (credits)


(46
)


1,810



6,581Asset impairment charges






4,645



6,853Total operating expenses


128,960



140,044



139,859INCOME (LOSS) FROM OPERATIONS


32,286



(17,829
)


(86,489
)INTEREST AND OTHER INCOME
    (EXPENSE), NET:Interest income


2,527



1,722



815Interest expense


(6,746
)


(6,747
)


(7,213
)Other income (expense), net


5,172



4,296



(237
)Interest and other income
    (expense), net


953



(729
)


(6,635
)INCOME (LOSS) BEFORE BENEFIT FROM
    (PROVISION FOR) INCOME TAXES AND MINORITY INTEREST


33,239



(18,558
)


(93,124
)BENEFIT FROM (PROVISION FOR)
    INCOME TAXES


(18,746
)


1,916



6,150MINORITY INTEREST


(14,597
)


(1,101
)


4,358NET LOSS

$
(104
)

$
(17,743
)

$
(82,616
)BASIC AND DILUTED NET LOSS PER
    SHARE

$
(0.00
)

$
(0.37
)

$
(1.98
)SHARES USED IN THE PER SHARE
    CALCULATION:Basic and diluted


47,972



47,441



41,805    53




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF SHAREHOLDERS EQUITY
  AccumulatedDeferred





OtherCommon Stock


Stock-Based


Accumulated


ComprehensiveShares


Amount


Compensation


Deficit


Income (Loss)


Total(As restated)


(As restated)


(As restated)





(As restated)(In thousands, except share data)BALANCES, MARCH 31, 2003, as
    previously reported


38,412,031


$
332,569


$
(3,992
)

$
(265,248
)

$
4,705


$
68,034Cumulative effect of restatement






18,713



(4,658
)


(19,467
)






(5,412
)BALANCES, MARCH 31, 2003, as
    restated


38,412,031



351,282



(8,650
)


(284,715
)


4,705



62,622Components of comprehensive loss:Net loss














(82,616
)






(82,616
)Foreign currency translation


















3,748



3,748Unrealized losses on investments


















(9
)


(9
)Total comprehensive loss






















(78,877
)Issuance of common stock from
    secondary stock offering, net of issuance costs of
    $5.7 million


6,900,000



98,945















98,945Issuance of common stock under
    employee stock option and employee stock purchase plans


1,859,717



13,194















13,194Deferred stock-based compensation
    related to stock option grants and the issuance of restricted
    stock to employees






2,279



(2,279
)










Tax benefit relating to stock
    options






2,213















2,213Amortization of deferred
    stock-based compensation










2,900











2,900Stock-based compensation expense
    relating to modification of stock options






189















189Non-employee stock-based
    compensation






1,066















1,066Reversal of deferred stock-based
    compensation due to forfeitures


(118,000
)


(3,262
)


3,262











BALANCES, MARCH 31, 2004, as
    restated


47,053,748



465,906



(4,767
)


(367,331
)


8,444



102,252Components of comprehensive loss:Net loss














(17,743
)






(17,743
)Foreign currency translation


















(842
)


(842
)Unrealized losses on investments


















(133
)


(133
)Total comprehensive loss






















(18,718
)Issuance of common stock under
    employee stock option and employee stock purchase plans


749,391



3,710















3,710Deferred stock-based compensation
    related to issuance of restricted stock to employees






1,240



(1,240
)










Amortization of deferred
    stock-based compensation










2,376











2,376Non-employee stock-based
    compensation






97















97Reversal of deferred stock-based
    compensation due to forfeitures


(23,600
)


(1,752
)


1,752











BALANCES, MARCH 31, 2005, as
    restated


47,779,539



469,201



(1,879
)


(385,074
)


7,469



89,717Components of comprehensive loss:Net income














(104
)






(104
)Foreign currency translation


















(6,946
)


(6,946
)Unrealized gains on investments


















231



231Total comprehensive loss






















(6,819
)Issuance of common stock under
    employee stock option and employee stock purchase plans


682,696



2,611















2,611Deferred stock-based compensation
    related to issuance of restricted stock to employees






1,389



(1,389
)










Amortization of deferred
    stock-based compensation










1,819











1,819Non-employee stock-based
    compensation






351















351Reversal of deferred stock-based
    compensation due to forfeitures






(130
)


130











BALANCES, MARCH 31, 2006


48,462,235


$
473,422


$
(1,319
)

$
(385,178
)

$
754


$
87,679    54




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)(In thousands)CASH FLOWS FROM OPERATING
    ACTIVITIES:NET LOSS

$
(104
)

$
(17,743
)

$
(82,616
)Adjustments to reconcile net loss
    to net cash provided by (used in) operating activities:Depreciation and amortization


23,339



28,442



28,843Non-cash restructuring charges










190Allowance for doubtful accounts


6,791



4,862



222Asset impairment charges






4,645



6,853Minority interest in net income
    (loss) of consolidated subsidiaries


14,597



1,101



(4,358
)Loss on disposal of fixed assets


876



571



431Stock-based compensation expense


2,170



2,473



4,155Amortization of lease incentive
    payments


(208
)






Deferred taxes, net


(4,929
)


(15,439
)


(6,394
)Changes in assets and liabilities,
    net of acquisitions:










Accounts receivable, net


29,081



(48,446
)


(59,370
)Inventories


(2,046
)


(5,206
)


(2,392
)Prepaid expenses and other assets


8,072



(5,645
)


1,222Accounts payable, accrued
    liabilities and deferred margin


(33,929
)


32,644



45,401Net cash provided by (used in)
    operating activities


43,710



(17,741
)


(67,813
)CASH FLOWS FROM INVESTING
    ACTIVITIES:Purchases of investments


(34,985
)


(84,744
)


(38,462
)Sales or maturity of investments


65,650



79,709



8,500Release of restricted cash and cash
    equivalents






1,904



1,403Purchases of property and equipment


(8,524
)


(4,152
)


(6,119
)Net proceeds from sale of land










12,106Net cash used in acquisitions






(31
)


(1,179
)Net cash provided by (used in)
    investing activities


22,141



(7,314
)


(23,751
)CASH FLOWS FROM FINANCING
    ACTIVITIES:Proceeds from line of credit


429,573



279,885



Payments to line of credit


(441,973
)


(271,519
)


(25,000
)Payments of short-term loans










(1,923
)Dividends paid to minority
    shareholder of ASI


(5,939
)






Principal payments on long-term
    debt and capital leases


(8,312
)


(7,920
)


1,939Proceeds from issuance of common
    stock


2,611



3,710



112,139Net cash provided by (used in)
    financing activities


(24,040
)


4,156



87,155Effect of exchange rate changes on
    cash and cash equivalents


(2,283
)


(414
)


(3,898
)INCREASE (DECREASE) IN CASH AND
    CASH EQUIVALENTS


39,528



(21,313
)


(8,307
)CASH AND CASH EQUIVALENTS,
    BEGINNING OF YEAR


55,094



76,407



84,714CASH AND CASH EQUIVALENTS, END OF
    YEAR

$
94,622


$
55,094


$
76,407Supplemental
    disclosures:Cash paid during the year for
    interest

$
6,229


$
5,690


$
6,751Cash paid (received) during the
    year for income taxes, net of refunds

$
14,380


$
3,153


$
(573
)    55




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL STATEMENTS
  1.
    Organization
    of the Company:            2.
    Results
    of Independent Directors Stock Option
    Investigation         56




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
                57




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     CONSOLIDATED
    BALANCE SHEET
  March 31, 2005(As reported)


(Adjustments)


(As restated)(In thousands, except share data)ASSETSCURRENT ASSETS:Cash and cash equivalents

$
55,094


$



$
55,094Short-term investments


46,086







46,086Accounts receivable, net


189,943







189,943Inventories


33,515







33,515Prepaid expenses and other current
    assets


33,971







33,971Total current assets


358,609







358,609Property and equipment, net


15,458







15,458Goodwill


64,014







64,014Intangible assets, net


40,898







40,898Other assets


4,795







4,795$
483,774


$



$
483,774LIABILITIES, MINORITY INTEREST
    AND SHAREHOLDERS EQUITYCURRENT LIABILITIES:Short-term loans and notes payable

$
20,563


$



$
20,563Current portion of long-term debt
    and capital leases


2,757







2,757Accounts payable


83,913







83,913Accounts payable-related parties


39,242







39,242Accrued and other liabilities


70,439



206



70,645Deferred margin


6,013







6,013Total current liabilities


222,927



206



223,133LONG-TERM LIABILITIESLong-term debt and capital leases,
    net of current portion


88,750







88,750Deferred tax liability


8,548







8,548Other long-term liabilities


9,771







9,771Total long-term liabilities


107,069







107,069COMMITMENTS AND CONTINGENCIESMINORITY INTEREST


63,855







63,855SHAREHOLDERS EQUITYCommon stock, no par value:Authorized shares 
    300,000,000Outstanding shares 
    47,779,539


450,005



19,196



469,201Deferred stock-based compensation


(1,312
)


(567
)


(1,879
)Accumulated deficit


(366,239
)


(18,835
)


(385,074
)Accumulated other comprehensive
    income


7,469







7,469Total shareholders equity


89,923



(206
)


89,717Total liabilities, minority
    interest and shareholders equity

$
483,774


$



$
483,774  58




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   CONSOLIDATED
    STATEMENTS OF OPERATIONS
  Fiscal Year Ended March 31,2005


2004(As reported)


(Adjustments)


(As restated)


(As reported)


(Adjustments)


(As restated)(In thousands, except per share data)NET SALES

$
612,987


$



$
612,987


$
301,642


$



$
301,642COST OF SALES


490,730



42



490,772



248,453



(181
)


248,272GROSS PROFIT


122,257



(42
)


122,215



53,189



181



53,370OPERATING EXPENSES:Research and development


34,747



62



34,809



36,376



(443
)


35,933Selling, general and administrative


78,247



97



78,344



70,541



(209
)


70,332Amortization of acquired intangible
    assets


20,436







20,436



20,160







20,160Restructuring and other charges
    (credits)


1,810







1,810



6,581







6,581Asset impairment charges


4,645







4,645



6,853







6,853Total operating expenses


139,885



159



140,044



140,511



(652
)


139,859INCOME (LOSS) FROM OPERATIONS


(17,628
)


(201
)


(17,829
)


(87,322
)


833



(86,489
)INTEREST AND OTHER INCOME
    (EXPENSE), NET:Interest income


1,722







1,722



815







815Interest expense


(6,746
)






(6,746
)


(7,213
)






(7,213
)Other income (expense), net


4,296







4,296



(237
)






(237
)Interest and other (expense), net


(729
)






(729
)


(6,635
)






(6,635
)LOSS BEFORE BENEFIT FROM INCOME
    TAXES AND MINORITY INTEREST


(18,357
)


(201
)


(18,558
)


(93,957
)


833



(93,124
)BENEFIT FROM INCOME TAXES


1,916







1,916



6,150







6,150MINORITY INTEREST


(1,101
)






(1,101
)


4,358







4,358NET LOSS

$
(17,542
)

$
(201
)

$
(17,743
)

$
(83,449
)

$
833


$
(82,616
)BASIC AND DILUTED NET LOSS PER SHARE

$
(0.37
)

$
(0.00
)

$
(0.37
)

$
(2.00
)

$
0.02


$
(1.98
)SHARES USED IN THE PER SHARE
    CALCULATION:Basic and diluted


47,441



47,441



47,441



41,805



41,805



41,805  59




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  2005


2004(As reported)


(Adjustments)


(As restated)


(As reported)


(Adjustments)


(As restated)(In thousands)CASH FLOWS FROM OPERATING
    ACTIVITIES:NET LOSS

$
(17,542
)

$
(201
)

$
(17,743
)

$
(83,449
)

$
833


$
(82,616
)Adjustments to reconcile net loss
    to net cash provided by (used in) operating activities:Depreciation and amortization


28,442







28,442



28,843







28,843Non-cash restructuring charges














190







190Allowance for doubtful accounts


4,862







4,862



222







222Asset impairment charges


4,645







4,645



6,853







6,853Minority interest in net income
    (loss) of consolidated subsidiaries


1,101







1,101



(4,358
)






(4,358
)Loss on disposal of fixed assets


571







571



431







431Stock-based compensation expense


1,621



852



2,473



2,646



1,509



4,155Amortization of lease incentive
    payments






















Deferred taxes, net


(15,439
)






(15,439
)


(6,394
)






(6,394
)Changes in assets and liabilities,
    net of acquisitions:






















Accounts receivable, net


(48,446
)






(48,446
)


(59,370
)






(59,370
)Inventories


(5,206
)






(5,206
)


(2,392
)






(2,392
)Prepaid expenses and other assets


(5,645
)






(5,645
)


1,222







1,222Accounts payable, accrued
    liabilities and deferred margin


33,295



(651
)


32,644



47,743



(2,342
)


45,401Net cash provided by (used in)
    operating activities


(17,741
)






(17,741
)


(67,813
)






(67,813
)CASH FLOWS FROM INVESTING
    ACTIVITIES:Purchases of investments (See
    Note 5)


(84,744
)






(84,744
)


(38,462
)






(38,462
)Sales or maturity of investments
    (See Note 5)


79,709







79,709



8,500







8,500Release of restricted cash and cash
    equivalents


1,904







1,904



1,403







1,403Purchases of property and
    equipment, net


(4,152
)






(4,152
)


(6,119
)






(6,119
)Net proceeds from sale of land














12,106







12,106Net cash used in acquisitions


(31
)






(31
)


(1,179
)






(1,179
)Net cash provided by (used in)
    investing activities


(7,314
)






(7,314
)


(23,751
)






(23,751
)CASH FLOWS FROM FINANCING
    ACTIVITIES:Proceeds from line of credit


279,885







279,885











Payments to line of credit


(271,519
)






(271,519
)


(25,000
)






(25,000
)Payments of short-term loans














(1,923
)






(1,923
)Principal payments on long-term
    debt and capital leases


(7,920
)






(7,920
)


1,939







1,939Proceeds from issuance of common
    stock


3,710







3,710



112,139







112,139Net cash provided by (used in)
    financing activities


4,156







4,156



87,155







87,155Effect of exchange rate changes on
    cash and cash equivalents


(414
)






(414
)


(3,898
)






(3,898
)INCREASE (DECREASE) IN CASH AND
    CASH EQUIVALENTS


(21,313
)






(21,313
)


(8,307
)






(8,307
)CASH AND CASH EQUIVALENTS,
    BEGINNING OF YEAR


76,407







76,407



84,714







84,714CASH AND CASH EQUIVALENTS, END OF
    YEAR (See Note 5)

$
55,094


$



$
55,094


$
76,407


$



$
76,407  60




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   3.
    Liquidity:    Form 10-K Form 10-Q
  Form 10-K Form 10-Q Forms 10-K 10-Q,
  Form 10-K Form 10-Q
  Form 10-Q Form S-3 Form S-3.
   61




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     4.
    Significant
    Accounting Policies:  Basis
    of Preparation
      Revisions
    to Prior Year Financial Statements
    Use of
    Estimates
    Foreign
    Currency Translation
   62




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Cash
    and Cash Equivalents
    Short-term
    Investments
  available-for-sale
  Fair
    Value of Financial Instruments
    Concentration
    of Credit Risk
   63




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Allowance
    for Doubtful Accounts
    Inventories
  (first-in,
  Goodwill
    and Other Intangible Assets
      Property
    and Equipment
    Land

noneBuildings

38 to 50 yearsLeasehold improvements

7 years or lease term, if
    shorterMachinery and equipment

2 to 5 yearsOffice equipment, furniture and
    fixtures

5 years  64




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Warranty
    Reserve
    Fiscal Year Ended March 31,2006


2005


2004Beginning Balance

$
13,509


$
8,185


$
7,561Reserve for warranties issued
    during the period


10,338



19,780



4,881Settlements made (in cash or in
    kind)


(14,966
)


(14,443
)


(4,257
)Foreign currency translation


(914
)


(13
)


Ending Balance

$
7,967


$
13,509


$
8,185   Revenue
    Recognition
  and/or
  Accounting for Performance of
    Construction-Type and Certain Production-Type Contracts.
  SOP 97-2, Software Revenue Recognition. percentage-of-completion
 65




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Income
    Taxes
        Net
    Income (Loss) Per Share
    Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)Basic and diluted net loss per
    share:Numerator:Net loss

$
(104
)

$
(17,743
)

$
(82,616
)Denominator:Weighted average common shares
    outstanding, excluding unvested restricted stock units


47,972



47,441



41,805Denominator for basic and diluted
    calculation


47,972



47,441



41,805Net loss per share, basic and
    diluted

$
(0.00
)

$
(0.37
)

$
(1.98
)  66




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004Restricted stock awards and units


9



136



59Stock options


6,879



6,827



8,212Convertible notes


5,682



5,682



5,682Total


12,570



12,645



13,953   Stock-Based
    Compensation
  Accounting for Stock
    Issued to Employees Accounting for Certain Transactions Involving Stock
    Compensation, an Interpretation of APB Opinion No. 25 Accounting for Stock
    Appreciation Rights and Other Variable Stock Option or Award
    Plans Accounting for Stock-Based Compensation Accounting for Stock Based
    Compensation  Transition and Disclosure 
    an amendment of FAS No. 123.
    Accounting for Equity Instruments That Are Issued to Other
    Than Employees for Acquiring, or in Conjunction with Selling,
    Goods or Services
 67




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)Net loss  as reported

$
(104
)

$
(17,743
)

$
(82,616
)Add: employee stock-based
    compensation expense included in reported net loss, net of tax


1,819



2,376



3,089Less: total employee stock-based
    compensation expense determined under fair value, net of tax


(6,838
)


(12,383
)


(14,436
)Net loss  as adjusted

$
(5,123
)

$
(27,750
)

$
(93,963
)Basic and diluted net loss per
    share  as reported

$
(0.00
)

$
(0.37
)

$
(1.98
)Basic and diluted net loss per
    share  as adjusted

$
(0.11
)

$
(0.58
)

$
(2.25
)SHARES USED IN THE PER SHARE
    CALCULATION:Basic and diluted


47,972



47,441



41,805   Recent
    Accounting Pronouncements
  Inventory Costs  an Amendment of ARB No. 43,
    Chapter 4
  Exchange of Nonmonetary Assets  an amendment of
    APB Opinion No. 29
     68




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##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        Accounting Changes and Error Corrections: a Replacement of
    Accounting Principles Board Opinion No. 20
    (APB 20) and FASB Statement No 3
  No. FAS 13-1, Accounting for Rental Costs Incurred during a Construction
    Period 13-1). 13-1 13-1
  FAS 115-1 FAS 124-1, The Meaning of
    Other-Than-Temporary
    Impairment and Its Application to Certain Investments, other-than-temporary other-than-temporary Not-for-Profit
 69




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Accounting for Uncertainty in Income Taxes: An Interpretation
    of FASB Statement No. 109
  No. 06-2, (EITF 06-2). EITF 06-2 EITF 06-2 EITF 06-02
    Fair Value Measurements
  Accounting for Defined Benefit Pension and Other
    Postretirement Plans  an amendment of FASB Statements
    No. 87, 88, 106, and 132(R not-for-profit
 70




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   5.
    Balance
    Sheet Components:  Cash
    and Cash Equivalents
      Unrealized2006

Cost


Gains (Losses)


Fair ValueInstitutional money market funds

$
19,656


$
100


$
19,756Commercial paper


2,994



(1
)


2,993Total cash equivalents

$
22,750


$
99


$
22,749   Unrealized2005

Cost


Loss


Fair ValueInstitutional money market funds

$
5,280


$



$
5,280Commercial paper


4,995



(1
)


4,994Total cash equivalents

$
10,275


$
(1
)

$
10,274   Short-term
    Investments
    UnrealizedCost


Loss


Fair ValueMarch 31, 2006Auction rate securities

$
8,300


$



$
8,300Corporate debt securities


6,014



(9
)


6,005Federal agency notes


1,000



(1
)


999$
15,314


$
(10
)

$
15,304March 31, 2005Auction rate securities

$
19,803


$



$
19,803Corporate debt securities


9,915



(47
)


9,868Municipal debt securities


501



(1
)


500International debt securities


1,009



(2
)


1,007Federal agency notes


15,000



(92
)


14,908$
46,228


$
(142
)

$
46,086   available-for-sale
  Due within one year

$
12,064Due within 39 years


3,250Total

$
15,314   other-than-temporary
 71




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      As Reported


As RevisedCash and Cash


Cash and CashEquivalents


EquivalentsMarch 31, 2004

$
101,907


$
76,407     As Reported


As RevisedSales/








Sales/Purchase of


Maturities of





Purchase of


Maturities ofAvailable for


Available for





Available for


Available forFiscal Year Ended

Sale Securities


Sale Securities


Net


Sale Securities


Sale Securities


NetMarch 31, 2005

$
(71,594
)

$
41,059


$
(30,535
)

$
(84,744
)

$
79,709


$
(5,035
)March 31, 2004

$
(12,962
)

$
8,500


$
(4,462
)

$
(38,462
)

$
8,500


$
(29,962
)   Accounts
    Receivable, net of allowance for doubtful accounts
    March 31,2006


2005Trade receivables

$
83,008


$
77,196Trade receivables-related party


90



100Unbilled receivables


63,435



110,778Other receivables


6,788



8,849Less: Allowance for doubtful
    accounts


(11,868
)


(6,980
)Total

$
141,453


$
189,943        72




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
       Inventories
    March 31,2006


2005Raw materials

$
9,882


$
14,040Work-in-process


22,180



17,905Finished goods


1,157



1,570Total

$
33,219


$
33,515       Prepaid
    expenses and other
    March 31,2006


2005Prepaid expenses

$
7,078


$
3,146Deferred tax assets


16,886



16,379Other


2,867



14,446Total

$
26,831


$
33,971  73




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Intangible
    assets
    March 31, 2006


March 31, 2005Gross








GrossCarrying


Accumulated





Carrying


AccumulatedAmount


Amortization


Net


Amount


Amortization


NetAmortizable intangible assets:Developed technology

$
58,289


$
44,275


$
14,014


$
62,626


$
34,069


$
28,557Customer base and other intangible
    assets


31,935



29,419



2,516



33,767



25,167



8,600Licenses and patents


6,316



3,512



2,804



6,989



3,248



3,741Total

$
96,540


$
77,206


$
19,334


$
103,382


$
62,484


$
40,898       Fiscal Year ending March 31,2007

$
11,9202008


5,9392009


6772010


3172011 and thereafter


481$
19,334   Goodwill
    Fab Automation


AMHS


TotalBalance at March 31, 2005

$
3,397


$
60,617


$
64,014Foreign currency translation






(5,174
)


(5,174
)Balances at March 31, 2006

$
3,397


$
55,443


$
58,840     Balances at March 31, 2004

$
71,973Purchase accounting adjustments


(6,953
)Foreign currency translation


(1,006
)Balances at March 31, 2005


64,014Foreign currency translation


(5,174
)Balances at March 31, 2006

$
58,840    74




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Property
    and Equipment
    March 31,2006


2005Land

$
2,115


$
2,312Buildings


7,332



8,231Leasehold improvements


21,174



12,608Machinery and equipment


29,325



28,050Office equipment, furniture and
    fixture


36,377



34,947Sub-total


96,323



86,148Less accumulated depreciation


(73,215
)


(70,690
)Total

$
23,108


$
15,458   Accrued
    and other liabilities
    March 31,2006


2005(As restated)Income taxes payable

$
23,818


$
18,378Other taxes payable


405



5,877Warranty reserve


7,967



13,509Contract loss reserve






248Restructuring reserve


105



883Employee compensation


9,308



8,822Customer deposits


1,984



2,918Other accrued expenses


19,315



20,010Total

$
62,902


$
70,645   Other
    long-term liabilities
    March 31,2006


2005Accrued pension benefit liability

$
6,975


$
9,463Lease Incentive


3,747



Other


252



308Total

$
10,974


$
9,771   Accumulated
    Comprehensive Income (Loss)
   75




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    March 31,2006


2005Unrealized gain (losses) on
    investments

$
89


$
(142
)Foreign currency translation
    adjustments


665



7,611Accumulated other comprehensive
    income

$
754


$
7,469   6.
    Restructuring
    and Other Charges (Credits):    Severance and


Excess


Fixed AssetsBenefits


Facilities


Impairment


TotalBalance, March 31, 2003

$
291


$
3,617


$
192


$
4,100Additional (reduction in) accruals


5,460



1,075



46



6,581Non-cash related utilization


70



(444
)


(205
)


(579
)Amounts paid in cash


(5,757
)


(2,058
)


(33
)


(7,848
)Balance, March 31, 2004


64



2,190







2,254Additional (reduction in) accruals


1,803



7







1,810Amounts paid in cash


(1,803
)


(1,390
)






(3,193
)Foreign currency translation
    adjustment


3



9







12Balance, March 31, 2005


67



816







883Additional (reduction in) accruals


(7
)


(39
)






(46
)Non-cash related utilization


(60
)


(96
)






(156
)Amounts paid in cash






(573
)






(573
)Foreign currency translation
    adjustment






(3
)






(3
)Balance, March 31, 2006

$



$
105


$



$
105        76




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    7.
    Asset
    Impairment Charges:  held-for-sale
  held-and-used.
    8.
    Income
    Taxes:    Fiscal Year Ended March 31,2006


2005


2004Domestic

$
(18,553
)

$
(25,004
)

$
(72,995
)Foreign


51,792



6,446



(20,129
)$
33,239


$
(18,558
)

$
(93,124
)     Fiscal Year Ended March 31,2006


2005


2004Current:Federal

$
(537
)

$
(334
)

$
State


41







31Foreign


22,671



15,388



2,272Total Current


22,175



15,054



2,303Deferred:Federal










State










Foreign


(3,429
)


(16,970
)


(8,453
)Total Deferred


(3,429
)


(16,970
)


(8,453
)Total provision for (benefit from)
    income taxes

$
18,746


$
(1,916
)

$
(6,150
)  77




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004Tax provision (or benefit) at
    federal statutory rate


35.0
%


(35.0
)%


(35.0
)%State taxes, net of Federal benefit


0.1
%


(3.9
)%


(5.7
)%Foreign income and withholding
    taxes in excess of statutory rate


3.4
%


(20.7
)%


0.9
%Non-deductible expenses and other


(1.4
)%


(1.4
)%


(0.8
)%Change in valuation allowance


19.3
%


50.7
%


40.0
%Effective income tax rate


56.4
%


(10.3
)%


(6.6
)%     Fiscal Year Ended March 31,2006


2005(As restated)Net operating loss and credit
    carryforwards

$
110,479


$
106,353Reserves and accruals


36,975



40,089Depreciation and Amortization


2,360



2,612Capitalized R&D


2,971



3,506Gross deferred tax assets


152,785



152,560Valuation allowance


(132,666
)


(130,211
)Net deferred tax assets

$
20,119


$
22,349Deferred tax liabilities:Intangible assets

$
(6,022
)

$
(12,748
)            78




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   9.
    Debt:      March 31,2006


2005Convertible subordinated notes

$
86,250


$
86,250Long-Tern loans


1,762



4,397Capital leases


524



860Total long-term debt


88,536



91,507Less: Current portion of long-term
    debt and capital leases


(1,368
)


(2,757
)Long-term debt and capital leases
    net of current portion

$
87,168


$
88,750     Fiscal Year Ending March 31,

Amount2007

$
1,3682008


7242009


86,4442010 and thereafter


$
88,536   Convertible
    Subordinated Notes
  3 4
  Form 10-K Form 10-Q
  Lines
    of Credit
   79




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
            10.
    Common
    Stock:    Employee Stock Option Plans


1,679,959Employee Stock Purchase Plan


116,2051,796,164   Sale
    of Equity Securities
   80




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Stock
    Option Plans
              Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)Cost of sales

$
157


$
281


$
267Research and development


179



406



1,062Selling, general and administrative


1,834



1,786



2,826$
2,170


$
2,473


$
4,155   out-of-the-money
 81




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004Weighted





Weighted





WeightedAverage





Average





AverageExercise





Exercise





ExerciseShares


Price


Shares


Price


Shares


PriceOptions outstanding, beginning of
    year


6,819,001


$
10.00



8,176,309


$
11.09



9,210,061


$
12.20Granted


1,671,083



5.73



1,699,250



7.17



3,014,508



6.67Exercised


(367,355
)


4.87



(460,148
)


5.64



(1,695,160
)


6.75Cancelled


(1,246,317
)


10.23



(2,596,410
)


12.35



(2,317,904
)


12.80Options outstanding, end of year


6,876,412


$
9.19



6,819,001


$
10.00



8,211,505


$
11.05Exercisable, end of year


4,522,974


$
10.74



4,674,163


$
11.37



4,417,856


$
12.40       Options Outstanding


Exercisable OptionsWeightedAverage


Weighted





WeightedNumber


Remaining


Average


Number


AverageRange of Exercise Prices

Outstanding


Contractual


Exercise Price


Exercisable


Exercise Price$ 0.00 - $ 3.95


1,249,039



5.61


$
3.79



640,610


$
3.714.13 -   4.94


845,556



5.23



4.72



242,970



4.704.98 -   5.05


727,167



6.90



5.04



454,339



5.055.09 -   8.02


724,721



6.47



6.45



426,630



6.558.19 -   9.65


722,539



5.81



9.08



434,145



8.949.75 -  11.25


691,431



6.96



10.26



524,189



10.2111.30 -  14.25


700,461



5.33



12.95



654,638



12.9014.40 -  19.06


899,298



5.48



17.32



829,253



17.4319.38 -  37.31


312,950



4.18



24.57



312,950



24.5751.38 -  51.38


3,250



4.03



51.38



3,250



51.38$ 0.00 - $51.38


6,876,412



5.83


$
9.19



4,522,974


$
10.74  82




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004Risk-free interest rate


4.7
%


3.4
%


3.0
%Expected term of options (in years)


3.3



4.6



4.7Expected volatility


83
%


91
%


81
%Expected dividend yield


0
%


0
%


0
%     Employee
    Stock Purchase Plan
      Fiscal Year Ended March 31,2006


2005


2004Risk-free interest rate


3.9
%


2.7
%


1.2
%Expected life (in years)


0.5



0.5



0.5Expected volatility


51
%


73
%


81
%Expected dividend yield


0
%


0
%


0
%   11.
    Employee
    Benefit Plans:  Defined
    Benefit Pension Plans
  and/or
 83




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005Change in projected benefit
    obligation:Beginning projected benefit
    obligation

$
18,842


$
18,703Acquisitions/Employee Transfers






132Service cost


781



738Interest cost


350



364Actuarial loss


135



1,268Currency exchange rate changes


(1,593
)


(280
)Benefits paid to plan participants


(1,641
)


(2,083
)Ending projected benefit
    obligation

$
16,874


$
18,842Change in Plan
    Assets:Beginning fair value of plan assets

$
7,300


$
6,153Actual return on plan assets


1,274



154Employer contributions


2,371



2,515Currency exchange rate changes


(722
)


(93
)Benefits paid to participants


(1,155
)


(1,429
)Ending fair value of plan
    assets

$
9,068


$
7,300Funded Status:Ending funded status

$
(7,806
)

$
(11,542
)Unrecognized net actuarial loss


831



1,912Net amount recognized

$
(6,975
)

$
(9,630
)Amounts Recognized in the
    Balance Sheet:Accrued pension liability

$
(6,975
)

$
(9,630
)     March 31,2006


2005Japanese equity securities


42.0
%


37.0
%Japanese debt securities


25.0
%


27.0
%Non-Japanese equity securities


22.0
%


21.0
%Non-Japanese debt securities


8.0
%


9.0
%Others


3.0
%


6.0
%Total


100.0
%


100.0
%  84




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Japanese equity securities

30% to 45%Japanese debt securities

20% to 30%Non-Japanese equity securities

20% to 30%Non-Japanese debt securities

10% to 20%Others

0% to 10%       March 31,2006


2005Discount rate


2.0%



2.0%Rate of compensation increase


2.5%



2.5%     Fiscal Year Ended March 31,2006


2005Discount rate


2.0%



2.0%Expected return on plan assets


3.5%



3.5%Rate of compensation increase


2.5%



2.5%       Fiscal Year Ended March 31,2006


2005


2004Company service cost

$
781


$
738


$
688Interest cost


350



364



352Expected return on plan assets


(266
)


(246
)


(243
)Amortization of unrecognized loss


2







Net periodic pension cost

$
867


$
856


$
797  85




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ending
    March 31,2007

$
8892008


1,5682009


2,5602010


2,4962011


2,1212012 through 2016


4,128Total

$
13,762         Employee
    Savings and Retirement Plan
    12.
    Reportable
    Segments:     86




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     March 31,2006


2005AMHS:Fixed Assets Additions, fiscal
    year ended

$
3,721


$
2,636Total Assets

$
251,477


$
312,391Fab Automation
    Products:Fixed Assets Additions, fiscal
    year ended

$
11,068


$
1,312Total Assets

$
163,817


$
171,383Consolidated:Fixed Assets Additions, fiscal
    year ended

$
14,789


$
3,948Total Assets

$
415,294


$
483,774   Fiscal Year Ended March 31,2006


2005


2004(As restated)


(As restated)AMHS:Net sales

$
294,483


$
380,596


$
168,510Cost of Sales


196,571



333,956



145,636Gross Profit

$
97,912


$
46,640


$
22,874Income (loss) from operations

$
47,782


$
844


$
(19,245
)Amortization and Depreciation

$
14,461


$
17,284


$
17,048Fab Automation
    Products:Net sales

$
164,738


$
232,391


$
133,132Cost of Sales


101,404



156,816



102,636Gross Profit

$
63,334


$
75,575


$
30,496Income (loss) from operations

$
(15,496
)

$
(18,673
)

$
(67,244
)Amortization and Depreciation

$
7,901


$
10,325


$
12,183Consolidated:Net sales

$
459,221


$
612,987


$
301,642Cost of Sales


297,975



490,772



248,272Gross Profit

$
161,246


$
122,215


$
53,370Income (loss) from operations

$
32,286


$
(17,829
)

$
(86,489
)Amortization and Depreciation

$
22,362


$
27,609


$
29,231    87




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Fiscal Year Ended March 31,2006


2005


2004United States

$
87,266


$
112,923


$
63,863Japan


183,079



146,752



83,778Taiwan


109,174



230,334



46,211Korea


21,123



30,240



45,785Other Asia/Pacific


27,336



70,879



41,381Europe


31,243



21,859



20,624Total

$
459,221


$
612,987


$
301,642     March 31,2006


2005United States

$
12,057


$
6,243Japan


12,992



11,915Other


312



324Total

$
25,361


$
18,482   13.
    Commitments
    and Contingencies:  Lease
    Commitments
    Fiscal Year Ending March 31,

Capital Lease


Operating Lease2007

$
231


$
3,2922008


162



3,1892009


148



1,5852010






1,4492011 and thereafter






4,238Total

$
541


$
13,753Less: interest


(17
)Present value of minimum lease
    payments


524Less: current portion of capital
    leases


(216
)Capital leases, net of current
    portion

$
308    88




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   Purchase
    Commitments
    Legal
    Commitments
         89




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    In re Asyst
    Technologies, Inc. Derivative Litigation Forlenzo v. Schwartz, et al et. seq. Rule 10b-5 Rule 14a-9
    Indemnifications
     90




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   14.
    Related
    Party Transactions:      March 31,2006


2005Accounts payable due to Shinko

$
13,406


$
39,221Accrued liabilities due to Shinko

$
59


$
450Accounts receivable from MECS Korea

$
90


$
100Accounts payable due to MECS Korea

$
3


$
21Accrued liabilities due to MECS
    Korea

$
81


$
     Fiscal Year Ended March 31,2006


2005


2004Material and service purchases
    from Shinko

$
57,043


$
96,097


$
42,511Material and service purchases
    from MECS Korea

$
3


$
414


$
2Sales to MECS Korea

$
568


$
378


$
138     15.
    Subsequent
    Events:  NASDAQ
    Delisting Proceedings
  Form 10-K Form 12b-25 Form 10-K
 91




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    
    On or before September 27, 2006, the Company submits
    supplemental information outlined in the letter concerning the
    previously announced Special Committee investigation into stock
    option grants and practices; and
    On or before November 30, 2006, the Company files its Form
    10-K for the
    fiscal year ended March 31, 2006, its
    Form 10-Q
    for the quarter ended June 30, 2006, and all required
    restatements (if any).    Acquisition
    and Related Debt Financing Facility
      3 4
        Notice
    of default relating to Convertible Subordinated
    Notes
  3 4 Form 10-K Form 10-Q
 92




---



##### Table of Contents



ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
     Form 10-K, Form 10-Q Forms 10-K 10-Q,
 93




---



##### Table of Contents



Report of
    Independent Registered Public Accounting Firm               Internal Control  Integrated
    Framework
     94




---



##### Table of Contents



95




---



##### Table of Contents



Supplementary
    Financial Data
    QUARTERLY
    FINANCIAL DATA
   Year Ended March 31, 2006First


Second


Third


FourthQuarter


Quarter


Quarter


Quarter(In thousands, except per share data)As reportedNet sales

$
117,451


$
124,595


$
106,824


$
110,351Gross profit


33,734



43,476



41,996



42,112Net income (loss)

$
(3,587
)

$
(1,545
)

$
2,979


$
2,437Basic net income (loss) per share

$
(0.08
)

$
(0.03
)

$
0.06


$
0.05Diluted net income (loss) per share

$
(0.08
)

$
(0.03
)

$
0.06


$
0.05Shares used in basic net income
    (loss) per share calculations


47,812



47,963



48,019



48,216Shares used in diluted net income
    (loss) per share calculations


47,812



47,963



48,789



50,178AdjustmentsNet sales

$



$



$



$
Gross profit


(26
)


(26
)


(20
)


Net income (loss)

$
(107
)

$
(91
)

$
(190
)

$
Basic net income (loss) per share

$
(0.00
)

$
(0.00
)

$
(0.00
)

$
(0.00
)Diluted net income (loss) per share

$
(0.00
)

$
(0.00
)

$
(0.00
)

$
(0.00
)Shares used in basic net income
    (loss) per share calculations


47,812



47,963



48,019



48,216Shares used in diluted net income
    (loss) per share calculations


47,812



47,963



48,789



50,178As restatedNet sales

$
117,451


$
124,595


$
106,824


$
110,351Gross profit


33,708



43,450



41,976



42,112Net income (loss)

$
(3,694
)

$
(1,636
)

$
2,789


$
2,437Basic net income (loss) per share

$
(0.08
)

$
(0.03
)

$
0.06


$
0.05Diluted net income (loss) per share

$
(0.08
)

$
(0.03
)

$
0.06


$
0.05Shares used in basic net income
    (loss) per share calculations


47,812



47,963



48,019



48,216Shares used in diluted net income
    (loss) per share calculations


47,812



47,963



48,789



50,178   96




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##### Table of Contents



Year Ended March 31, 2005First


Second


Third


FourthQuarter


Quarter


Quarter


QuarterAs reportedNet sales

$
139,425


$
168,606


$
161,383


$
143,573Gross profit


27,095



30,848



27,569



36,745Net loss

$
(2,286
)

$
(1,831
)

$
(11,644
)

$
(1,781
)Basic and diluted net loss per
    share

$
(0.05
)

$
(0.04
)

$
(0.24
)

$
(0.04
)Shares used in basic and diluted
    net loss per share calculations


47,179



47,428



47,553



47,678AdjustmentsNet sales

$



$



$



$
Gross profit


(21
)


(15
)


(1
)


(5
)Net income (loss)

$
(98
)

$
(56
)

$
(27
)

$
(20
)Basic and diluted net income
    (loss) per share

$
(0.00
)

$
(0.00
)

$
(0.01
)

$
(0.00
)Shares used in basic and diluted
    net loss per share calculations


47,179



47,428



47,553



47,678As restatedNet sales

$
139,425


$
168,606


$
161,383


$
143,573Gross profit


27,074



30,833



27,568



36,740Net loss

$
(2,384
)

$
(1,887
)

$
(11,671
)

$
(1,801
)Basic and diluted net loss per
    share

$
(0.05
)

$
(0.04
)

$
(0.25
)

$
(0.04
)Shares used in basic and diluted
    net loss per share calculations


47,179



47,428



47,553



47,678                  97




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##### Table of Contents



Form 10-K
  Item 9 
    Changes
    in and Disagreements with Accountants on Accounting and
    Financial Disclosure    Item 9A  
    Controls
    and Procedures  Special
    Committee Investigation into Past Option Grants and Practices
    and Restatement
  Background
    Findings and Restatement
    Special
    Committees Investigation: Scope, Report and
    Findings
         98




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##### Table of Contents



Corrected
    Measurement Dates and Determination to Restate
        Managements
    Conclusion Regarding the Effectiveness of Internal Controls over
    Stock Option Grant Practices
    Managements
    Consideration of the Restatement
   99




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##### Table of Contents




    consistent practices for the approval of all stock option grants
    by the Compensation Committee
    high level of objectivity in determination of pricing of stock
    option grants made to all employees
    greater advance review and certification of proposed option
    grants to ensure proper accounting and compliance with the
    applicable stock plan terms and conditions
    consistent use of improved stock option grant approval
    documentation
    increased review of Company stock option grant plans and
    approval processes and documentation by the Companys
    counsel (internal and outside)
    increased review by the Compensation Committee of the
    Companys stock option grant practices
    use of outside consultants to review the Companys stock
    option grant practices
    quarterly internal reconciliations of stock option grant
    activities
    use of additional training resources for personnel in areas
    associated with the stock option granting processes to increase
    competency levels of the personnel involved
    greater use of restricted stock awards (as opposed to option
    grants) as components of the Companys overall equity
    incentive and compensation programs.    Evaluation
    of Disclosure Controls and Procedures
  Rule 13a-15(e)
  Form 10-K
 100




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##### Table of Contents



Form 10-K Form 10-K
  Managements
    Report on Internal Control over Financial Reporting
  Rule 13a-15(f)
  Internal
    Control  Integrated Framework
        Internal Control 
    Integrated Framework
   101




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##### Table of Contents



Managements
    Remediation Initiatives
      Form 10-K
             102




---



##### Table of Contents



Changes
    in Internal Control over Financial Reporting
  Special
    Committees Recommended Further Measures Regarding Stock
    Option Grants
    
    reduce the number of occasions on which options are granted
    Compensation Committee meetings to approve option grants should
    be regularly scheduled, and the committee should minimize the
    use of unanimous written consents
    option grants approved at Compensation Committee meetings should
    be effective two business days after the release of quarterly
    earnings results
    the Companys finance department should provide greater
    advance review and certification of proposed option grants to
    ensure proper accounting and compliance with the applicable
    stock plan terms and conditions
    the Company should improve documentation of option grant
    approvals and approved grants should be promptly entered into
    the Companys financial records and stock option database
    the Compensation Committee should be provided with enhanced
    technical support to ensure proper accounting and compliance
    with the applicable stock plan terms and conditions
    the Companys stock administration personnel should receive
    regular training, and the finance and internal audit functions
    should regularly review stock option grant records and processes 103




---



##### Table of Contents




    the Companys management should report quarterly to the
    Companys Audit Committee that the Companys stock
    option grants comply with internal procedures, proper accounting
    principles, and applicable SEC disclosure requirements
    a member of the Special Committee should be added to the
    Compensation Committee to provide for an efficient transfer of
    the information obtained by the Special Committee through its
    investigative process Item 9B 
    Other Information   PART III Item 10 Directors and Executive Officers of the Registrant  Directors
    Name

Age

Principal OccupationStephen S.
    Schwartz, Ph.D.


46


Chair of our Board of Directors,
    President and Chief Executive Officer of AsystStanley Grubel


64


Retired Vice President and General
    Manager, Philips Semiconductor Manufacturing, Inc., and retired
    CEO of MiCRUSTsuyoshi Kawanishi


77


Retired Executive Senior Vice
    President and Director, Toshiba Electronic Co., Ltd.Robert A. McNamara


52


President and Chief Executive
    Officer, LVI Services, Inc.Anthony E. Santelli


66


Retired Executive Vice Chairman,
    USA Global Link, and retired General Manager, IBMWilliam Simon


68


Retired Executive Vice President,
    BearingPoint, Inc., and retired National Managing Partner, KPMG
    LLPWalter W. Wilson


62


Retired Senior Vice President,
    Solectron Corporation   Dr. Schwartz
  Mr. Grubel
 104




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##### Table of Contents



Mr. Kawanishi
  Mr. McNamara
  Mr. Santelli
  Mr. Simon 37-year
  Mr. Wilson
    Governance andAudit


Nominating


CompensationDirector Name and Positions

Committee


Committee


CommitteeStephen S. Schwartz (Chairman,
    Chief Executive Officer and President)










Stanley Grubel (Director)


X



Chair



XTsuyoshi Kawanishi (Director)










Robert A. McNamara (Director)


X







Anthony E. Santelli (Director)










ChairWilliam Simon (Director)


Chair







Walter W. Wilson (Director)


X



X



X  105




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##### Table of Contents



Executive
    Officers
    Name

Age

Principal OccupationStephen S. Schwartz


46


Chair of the Board, Chief
    Executive Officer and PresidentAnthony C. Bonora


63


Executive Vice President, Research
    and Development, Chief Technical Officer and Asyst FellowAlan S. Lowe


44


Senior Vice President, Global
    Business SolutionsSteve Debenham


44


Vice President, General Counsel
    and SecretaryRichard H. Janney


48


Interim Chief Financial Officer
    and interim Principal Accounting Officer     Mr. Bonora
  Mr. Lowe 2000-2003, 2000-2001, 1997-2000.
  Mr. Debenham
  Mr. Janney interim
 106




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##### Table of Contents



2000-2002 (1984-1992),
    Audit
    Committee
  Charter and Purposes. www.asyst.com
  Members.
  Audit Committee Financial Expert.
  Section 16(a)
    Beneficial Ownership Reporting Compliance
      Code of
    Ethics
   107




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##### Table of Contents



Item 11 
    Executive Compensation  Summary
    of Compensation
    Long Term Compensation AwardsAwards


PayoutsAnnual Compensation


Restricted


Securities


LTIP


All OtherFiscal


Salary


Bonus


Stock


Underlying


Payouts


CompensationName and Principal Position

Year


($)


($)(1)


Awards ($)(2)


Options (#)


($)


($)Stephen S. Schwartz(3)


2006



362,885



450,000



276,500



100,000







2,938
(4)

Chairman of the Board,


2005



330,000











100,000







1,098
(5)President and Chief


2004



305,692











280,000







809
(5)

Executive OfficerAnthony C. Bonora


2006



270,963



150,000



128,375



30,000







223,931
(6)Executive Vice President,


2005



260,000



30,675







60,000







200,012
(7)Research and


2004



245,000











115,000







18,500
(8)DevelopmentChief Technical OfficerAlan S. Lowe


2006



166,154



150,000



186,400



220,000







381
(5)Senior Vice President,


2005


























Global Business Solutions


2004























Robert J. Nikl(9)


2006



265,000



140,000



128,200



25,000







1,325
(5)Senior Vice President,


2005



135,558











200,000







556
(5)Chief Financial Officer


2004























Steve Debenham


2006



223,656



100,000



88,875



35,000







778
(10)Vice President,General


2005



214,988











50,000







651
(11)

Counsel and Secretary


2004



115,500



45,000
(12)






100,000







256
(11)     (1)
    
    Our officers are eligible for annual cash bonuses under the
    terms of our Executive Bonus Plan. Payments of bonuses are based
    upon achievement of specified company financial and individual
    performance objectives determined at the beginning of each
    fiscal year by our Board and its Compensation Committee. Company
    financial objectives are based, in part, on our operating budget
    and results of operations.(2)
    
    These amounts represent the closing market value of the awarded
    shares of restricted stock, determined as of the date of grant.    Total Unvested


Value as ofNamed Executive Officer

Restricted Shares Held (#)


March 31, 2006 ($)Stephen S. Schwartz


53,333



555,197Anthony C. Bonora


24,999



260,240Alan S. Lowe


40,000



416,400Robert J. Nikl


30,833



320,972Steve Debenham


16,666



173,493  108




---



##### Table of Contents



Award


Award


Award


Award


AwardName

Type A(A)


Type B(B)


Type C(C)


Type D(D)


Type E(E)Schwartz


33,333



20,000



0



0



0Bonora


14,999



10,000



0



0



0Lowe


0



0



30,000



10,000



0Nikl (F)


8,333



7,500



0



0



15,000Debenham


11,666



5,000



0



0



0     (A)
    
    Vests in increments of one half on each of March 31, 2007,
    and May 16, 2008.(B)
    
    Vests, if at all, on May 16, 2008, as to 100% of the shares
    if Asysts market capitalization has appreciated relative
    to the top one-third of an identified group of semiconductor
    capital equipment companies determined to be comparable to
    Asyst, 50% of the shares if Asysts market capitalization
    has appreciated relative to the middle one-third of that group,
    and none of the shares if Asysts market capitalization has
    only appreciated relative to the bottom one-third of that group
    (with the measurement of the relative market capitalization
    performance to be made as of March 31, 2008).(C)
    
    Vests in increments of one-third on each of August 31,
    2006, August 31, 2007, and August 31, 2008.(D)
    
    Vests, if at all, on August 31, 2008, as to 100% of the
    shares if Asysts market capitalization has appreciated
    relative to the top one-third of an identified group of
    semiconductor capital equipment companies determined to be
    comparable to Asyst, 50% of the shares if Asysts market
    capitalization has appreciated relative to the middle one-third
    of that group, and none of the shares if Asysts market
    capitalization has only appreciated relative to the bottom
    one-third of that group (with the measurement of the relative
    market capitalization performance to be made as of
    March 31, 2008).(E)
    
    Vests in increments of one-half on each of April 29, 2008
    and April 29, 2009(F)
    
    Upon Mr. Nikls termination of employment as of
    June 30, 2006, the unvested restricted shares allocated to
    him in the table above were deemed cancelled.  (3)
    
    Dr. Schwartz was appointed our President and Chief
    Executive Officer in August 2002 and the Chair of our Board in
    January 2003.(4)
    
    Consists of a five-year service award of $1,500, premiums for
    term life insurance and supplemental disability insurance
    totaling $1,160 and an in-kind service award valued at $278.(5)
    
    Consists of premiums for term life and supplemental disability
    insurance.(6)
    
    Consists of (i) a $222,018 distribution of previously
    earned salary but deferred to our Executive Deferred
    Compensation Program, (ii) payments totaling $1,501 under
    our inventor incentive compensation program as consideration for
    assignment to us of rights to patentable inventions developed
    during employment, (iii) a payment of $100 as a special
    recognition award, and (iv) an in-kind service award valued
    at $312.(7)
    
    Consists of (i) a $197,679 distribution of previously
    earned salary but deferred to our Executive Deferred
    Compensation Program and (ii) payments of $2,333 under our
    inventor incentive compensation program as consideration for
    assignment to us of rights to patentable inventions developed
    during employment.(8)
    
    Consists of payments under our inventor incentive compensation
    program as consideration for assignment to us of rights to
    patentable inventions developed during employment.(9)
    
    Mr. Nikl gave us notice on May 26, 2006, that he would
    be resigning as our Chief Financial Officer effective as of
    June 19, 2006 and leaving Asyst on June 30, 2006.(10)
    
    Consists of (i) premiums for term life and supplemental
    disability insurance totaling $474 and (ii) an in-kind
    service award valued at $304.(11)
    
    Consists of premiums for term life, supplemental disability
    insurance, and health club membership dues.(12)
    
    Consists of a sign-on bonus. 109




---



##### Table of Contents



Stock
    Option Grants and Exercises
      Option
    Grants in Last Fiscal Year
  Percentage of








Potential RealizableTotal Options








Value at AssumedNumber of


Granted to








Annual Rates of StockSecurities Underlying


Employees in


Exercise





Price Appreciation forOptions Granted


Fiscal Year


Price


Expiration


Option Term(3)Name

(#)


(1)


($/Sh)(2)


Date


5%($)


10%($)Stephen S. Schwartz


50,000
(4)


2.99
%


3.95



5/15/2011



67,169



152,38350,000
(5)


2.99
%


3.95



5/15/2011



67,169



152,384100,000



5.98
%










134,338



304,767Anthony C. Bonora


30,000
(4)


1.80
%


3.95



5/15/2011



40,301



91,340Alan S. Lowe


220,000
(6)


13.17
%


4.81



8/30/2011



359,889



816,466Robert J. Nikl


25,000
(4)


1.50
%


3.95



5/15/2011



33,584



76,192Steve Debenham


10,000
(4)


0.60
%


3.95



5/15/2011



13,434



30,47625,000
(7)


1.50
%


4.13



5/26/2011



35,115



79,66435,000



2.10
%










48,549



110,140     (1)
    
    Based on an aggregate of 1,671,083 options awarded to directors
    and employees of Asyst in fiscal year 2006, including the Named
    Executive Officers.(2)
    
    The exercise price per share of each option is equal to the fair
    market value of the underlying stock on the date of the award.(3)
    
    The potential realizable value is calculated based on the
    six-year terms of the options. It is calculated by assuming that
    the stock price on the date of award appreciates at the
    indicated annual rate, compounded annually for the entire term
    of the option, and that the option is exercised and sold on the
    last day of its term for the appreciated stock price.(4)
    
    Consists of options that vest in the following increments:
    one-third on each of March 31, 2006, March 31, 2007,
    and May 16, 2008.(5)
    
    Consists of options that vest as of the date the closing price
    of the Companys common stock reported on NASDAQ has been
    $15.00 or more for each of ten consecutive days.(6)
    
    Consists of options that vest in the following increments:
    one-third on August 31, 2006, one-third on August 31,
    2007, and one-third on August 31, 2008.(7)
    
    Consists of options that vest in full as of December 31,
    2006. 110




---



##### Table of Contents



Aggregated
    Option Exercises in Last Fiscal Year and
    Fiscal Year-End Option Values, as of March 31,
    2006
  Number of Securities


Value of UnexercisedShares


Value


Underlying Unexercised


In-the-Money
    OptionsAcquired on


Realized


Options at FY-End (#)


at FY-End ($)Name

Exercise (#)


($)(1)


Exercisable/Unexercisable


Exercisable/Unexercisable(2)Stephen S. Schwartz


0



0



752,917/252,083



1,259,886/1,257,581Anthony C. Bonora


95,000



401,382



360,747/101,250



831,207/426,750Alan S. Lowe


0



0



0/220,000



0/1,232,000Robert J. Nikl(3)


0



0



58,334/166,666



350,671/928,162Steve Debenham


0



0



108,691/76,309



167,417/172,350     (1)
    
    Based on the fair market value of our common stock as of the
    date of exercise, minus the exercise price of the option.(2)
    
    Based on the fair market value of our common stock as of
    March 31, 2006, which was $10.41, minus the exercise price
    of the option.(3)
    
    In light of Mr. Nikls termination of employment as of
    June 30, 2006, all of his unexercised options have been
    cancelled.  Employment,
    Severance and Change of Control Agreements
    1 42
    and/or
 111




---



##### Table of Contents



out-of-pocket
       112




---



##### Table of Contents



Director
    Compensation
  de
    minimis
  Sign-on equity award.
  Annual equity award.
  Director cash retainer and board meeting
    fees.
  
    a $35,000 annual cash retainer, or a pro-rata portion thereof,
    for service on our Board, and
    $2,000 for each Board meeting attended in person and $1,000 if
    attended telephonically.  Committee cash retainer and committee meeting
    fees.
  
    a $5,000 annual cash retainer, or pro-rated portion thereof, and
    $1,000 for each committee meeting attended in person and $500 if
    attended telephonically (including for service on Special
    Committees).  Committee chair cash fees.
  Other fees and reimbursements.
 113




---



##### Table of Contents



Committee





Total


StockAnnual


Committee


All Meeting


Chair/Financial


Other


Cash


AwardsNon-employee Director

Retainer


Retainer(s)


Fees(1)


Expert Fees


Payments


Payments


($)(2)Stanley Grubel

$
35,000


$
15,000


$
29,000


$
7,500






$
86,500


$
60,840Tsuyoshi Kawanishi

$
35,000






$
13,000






$
40,829
(3)

$
88,829


$
60,840Robert A. McNamara

$
35,000


$
5,000


$
17,000










$
57,000


$
60,840Anthony E. Santelli

$
35,000


$
5,000


$
22,000


$
7,500






$
69,500


$
60,840William Simon(4)

$
35,000


$
5,000


$
28,000



5,000






$
73,000


$
60,840Walter W. Wilson(5)

$
35,000


$
10,000


$
25,000



5,000






$
75,000


$
60,840     (1)
    
    Includes cash attendance fees for meetings of the Board of
    Directors and committees on which the individual serves,
    including meetings of a Special Committee, in fiscal year 2006.(2)
    
    Represents the value as of April 1, 2005, of the number of
    shares underlying restricted stock awarded as the annual stock
    award for fiscal year 2006 to non-employee directors, having
    vesting and other terms summarized above. No director joined the
    board during fiscal 2006, and therefore no sign-on stock was
    awarded.(3)
    
    Represents a $5,000 annual retainer for service as a director of
    our majority-owned subsidiary Asyst Japan, Inc. and consulting
    fees of JPY400,000 paid monthly for services directly to that
    subsidiary (such consulting fees totaled US$40,829 for fiscal
    year 2006, based on March 31, 2006 exchange rates).(4)
    
    Mr. Simon is designated as our audit committee financial
    expert, and beginning October 1, 2005 is Chair of the Audit
    Committee.(5)
    
    Mr. Wilson served as Chair of the Audit Committee through
    September 30, 2005.  de minimis
  Item 12 
    Security
    Ownership of Certain Beneficial Owners and Management and
    Related Stockholder Matters  SECURITY
    OWNERSHIP OF
    CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
    
    each incumbent director;
    each of our named executive officers;
    all of our named executive officers and incumbent directors as a
    group; and
    all those known by Asyst to be beneficial owners of more than
    five percent (5%) of our common stock.   114




---



##### Table of Contents



BeneficialOwnership(1)Number of


Percent ofBeneficial Owner

Shares (#)


Total (%)Wellington Management Company
    LLP(2)


6,681,000



13.6
%75 State Street 
    Boston, MA 02109Alexandra Global Master
    Fund L.P.(3)


4,808,959



9.8
%767 Third Avenue, 39th Floor
    
    New York, NY 10017Stephen S. Schwartz(4)


956,767



2.0
%Anthony C. Bonora(5)


434,567



*Alan S. Lowe(6)


73,334



*Robert J Nikl(7)


2,503



*Steve Debenham(8)


165,180



*Stanley Grubel(9)


121,164



*Tsuyoshi Kawanishi(10)


72,922



*Robert A. McNamara(11)


79,944



*Anthony E. Santelli(12)


73,978



*William Simon(13)


39,315



*Walter W. Wilson(14)


109,664



*All current directors and named
    executive officers as a group (11 persons)(15)


2,129,338



4.3
%     *
    
    Less than one percent.(1)
    
    This table is based upon information supplied by officers,
    directors and principal shareholders, and Schedules 13G filed
    with the SEC. Schedule 13G provides information as to
    beneficial ownership only as of their dates of filing, and,
    consequently, the beneficial ownership of Asysts principal
    shareholders may have changed between such dates and
    August 31, 2006. Unless otherwise indicated in the
    footnotes to this table, and subject to community property laws
    where applicable, Asyst believes that each of the shareholders
    named in this table has sole voting and investment power with
    respect to the shares indicated as beneficially owned.(2)
    
    In an amended Schedule 13G filed February 14, 2006,
    Wellington Management Company LLP, in its capacity as investment
    adviser, reports shared voting power over 3,479,000 shares,
    and shared dispositive power over 6,681,000 shares, which
    are reportedly held of record by clients of Wellington
    Management Company LLP.(3)
    
    In a Schedule 13G filed December 12, 2005, Alexandra
    Global Master Fund Ltd. reports shared voting and
    dispositive power over 4,715,744 shares, and Alexandra
    Investment Management, LLC, Mikhail A. Filimonov, and Dimitri
    Sogoloff each report shared voting and dispositive power over
    4,808,959 shares. That Schedule 13G also reported that
    of the total shares reported, 4,715,744 are shares of common
    stock that Alexandra Global Master Fund Ltd. has the right
    to acquire upon conversion of 5.75% Convertible
    Subordinated Notes Due 2008 issued by Asyst.(4)
    
    Includes 834,167 shares subject to stock options
    exercisable within 60 days after August 31, 2006.(5)
    
    Includes 402,000 shares subject to stock options
    exercisable within 60 days after August 31, 2006.(6)
    
    Consists of 73,334 shares subject to stock options
    exercisable within 60 days of August 31, 2006.(7)
    
    Mr. Nikl gave us notice on May 26, 2006, that he would
    be resigning as our Chief Financial Officer effective as of
    June 19, 2006 and leaving Asyst on June 30, 2006. The
    figure in the table is his estimated beneficial ownership as of
    August 31, 2006.(8)
    
    Includes 122,977 shares subject to stock options
    exercisable within 60 days after August 31, 2006.(9)
    
    Includes 99,500 shares subject to stock options exercisable
    within 60 days after August 31, 2006. Excludes
    1,750 shares represented by restricted stock units whose
    distribution Mr. Grubel has elected to defer. 115




---



##### Table of Contents



(10)
    
    Includes 49,508 shares subject to stock options exercisable
    within 60 days after August 31, 2006.(11)
    
    Includes 47,500 shares subject to stock options exercisable
    within 60 days after August 31, 2006.(12)
    
    Includes 39,062 shares subject to stock options exercisable
    within 60 days after August 31, 2006.(13)
    
    Excludes 1,313 shares represented by restricted stock units
    whose distribution Mr. Simon has elected to defer.(14)
    
    Includes 91,500 shares subject to stock options exercisable
    within 60 days after August 31, 2006. Excludes
    5,250 shares represented by restricted stock units whose
    distribution Mr. Wilson has elected to defer.(15)
    
    Includes 1,759,548 shares beneficially owned by all current
    directors and executive officers that are subject to options
    exercisable within 60 days after August 31, 2006.
    Excludes 8,313 shares represented by restricted stock units
    whose distribution the recipient has elected to defer.  EQUITY
    COMPENSATION PLAN INFORMATION
    Number of SecuritiesNumber of





Remaining AvailableSecurities





for Issuance Underto be Issued Upon


Weighted-Average


Equity CompensationExercise of


Exercise Price of


Plans (ExcludingOutstanding Options,


Outstanding Options,


Securities Reflected inWarrants and Rights


Warrants and Rights


Column (a))Plan Category

(a)(1)


(b)


(c)Equity compensation plans approved
    by security holders


5,301,668
(2)

$
9.55
(3)


1,703,439
(4),(5)Equity compensation plans not
    approved by security holders


1,583,931
(6)

$
8.01



92,725Total


6,876,412


$
9.20



1,796,164
(7)     (1)
    
    Column (a) does not include shares of restricted stock that
    are deemed outstanding, but does include shares underlying
    restricted stock units outstanding as of March 31, 2006,
    that may be delivered in the future upon satisfaction of
    applicable vesting requirements and deferral arrangements. The
    weighted average exercise price in column (b) does not
    account for shares underlying these latter awards that have no
    exercise price.(2)
    
    We have four equity compensation plans approved by shareholders
    under which awards remain outstanding: 2003 Incentive Plan, 1993
    Employee Stock Option Plan, 1993 Non-Employee Directors
    Stock Plan, and 1993 Employee Stock Purchase Plan. The column
    (a) number does not include Purchase Plan shares or
    previously issued shares of restricted stock. The column
    (a) number (i) does include 9,187 shares of
    common stock that are issuable under restricted stock units that
    have been granted but have not yet vested but (ii) does not
    include shares issued under granted stock awards.(3)
    
    This calculation does not take into account either
    (i) granted but unvested stock units with no exercise price
    or (ii) granted stock awards.(4)
    
    Of these shares, 116,205 remain available as of March 31,
    2006 for purchase under our Purchase Plan, and 1,587,234 remain
    available as of March 31, 2006 for issuance under future
    awards from our 2003 Plan. The latter number does not include
    the indefinite number of additional shares that may become
    available for future award under the 2003 Plan due to
    cancellations of options or other expirations or forfeitures
    that by the terms of the applicable plan are added back to the
    available share reserve. The 2003 Plan currently provides that
    up to 30% of the shares authorized for issuance may be awarded
    as restricted stock.(5)
    
    The 1993 Employee Stock Option Plan and 1993 Non-Employee
    Directors Stock Plan have expired or been terminated, and
    no shares remain available for issuance as future awards under
    those expired or terminated plans.(6)
    
    This total includes 1,981 shares issuable under outstanding
    options as of March 31, 2006, with a weighted average
    exercise price of $2.19 that we assumed or otherwise issued
    outside of our other equity compensation 116




---



##### Table of Contents



plans in connection with our acquisition of other companies. No
    additional options may be awarded under any plans or other
    arrangements assumed in these acquisitions.(7)
    
    These shares represent the number of shares available for
    issuance as of March 31, 2006 under future awards of stock
    options or restricted stock from the 2001 Non-Officer Equity
    Plan, described below. This number does not include the
    indefinite number of additional shares that may become available
    for future award due to cancellations of options or other
    expirations or forfeitures that by the terms of the applicable
    plan are added back to the available share reserve.  2001
    Non-Officer Equity Plan
    Eligibility for Participation.
  Terms of Options.
    Terms of Stock Bonuses and Purchases of Restricted
    Stock.
  Effect of Certain Corporate Events.
 117




---



##### Table of Contents



Item 13 
    Certain Relationships and Related Transactions   Item 14 
    Principal Accountant Fees and Services    March 31,


March 31,Fee Category

2006


2005Audit Fees

$
4,822,886


$
4,721,992Audit-Related Fees






Tax Fees


458,391



414,260All Other Fees






Total Fees

$
5,281,277


$
5,136,252   Audit Fees: Form 10-K, Form 10-Q, non-U.S. jurisdictions.
  Audit-Related Fees:
  Tax Fees:
  All Other Fees:
   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
  Form 10-K.
  Financial Statement Schedule
  Form 10-K.
 118




---



##### Table of Contents



Exhibits
  Form 10-K.
  Exhibits
  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 Incorporation, filed
    October 5, 2000.


DEF 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

7/19/1993 119




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.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

11/12/200210
.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.













X10
.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

8/5/2004 120




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.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.













X10
.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

6/29/200510
.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)













X10
.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

2/6/2006 121




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.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.













X10
.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.













X10
.39*

Separation Agreement and Release
    of All Claims between the Company and Warren C. Kocmond, dated
    May 31, 2006.













X10
.40*

Change-in-Control
    Agreement between the Company and Steve Debenham, dated
    May 22, 2006.













X10
.41*

Change-in-Control
    Agreement between the Company and Alan S. Lowe, dated
    May 22, 2006













X10
.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.













X21
.1

Subsidiaries of Asyst
    Technologies, Inc.













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).













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 122




---



##### Table of Contents



SCHEDULE II
  ASYST
    TECHNOLOGIES, INC. AND SUBSIDIARIES
  VALUATION
    AND QUALIFYING ACCOUNTS
  Balance








ForeignBeginning


Charged to





Currency


Balanceof Year


Expenses


Deductions


Translation


End of Year(In thousands)Allowance for doubtful
    accountsYear Ended March 31,2004

$
4,880


$
222


$
(494
)

$



$
4,6082005

$
4,608


$
4,862


$
(2,490
)

$



$
6,9802006

$
6,980


$
6,791


$
(1,249
)

$
(654
)

$
11,868  123




---



##### Table of Contents



SIGNATURES      By:
    /s/  RICHARD
    H. JANNEY    Interim Chief Financial Officer
      Signature

Title

Date/s/  STEPHEN
    S. SCHWARTZ, PH.
    D.Stephen
    S. Schwartz, Ph. D.

Chairman of the Board, 
    Chief Executive Officer and Director 
    (Principal Executive Officer)

October 13, 2006/s/  RICHARD
    H. JANNEYRichard
    H. Janney

Interim Chief Financial Officer
    
    (and Interim Principal Accounting Officer)

October 13, 2006/s/  STANLEY
    GRUBELStanley
    Grubel

Director

October 13, 2006/s/  TSUYOSHI
    KAWANISHITsuyoshi
    Kawanishi

Director

October 13, 2006/s/  ROBERT
    A. MCNAMARARobert
    A. McNamara

Director

October 13, 2006/s/  ANTHONY
    E. SANTELLIAnthony
    E. Santelli

Director

October 13, 2006/s/  WILLIAM
    SIMONWilliam
    Simon

Director

October 13, 2006/s/  WALTER
    W. WILSONWalter
    W. Wilson

Director

October 13, 2006  124




---



##### Table of Contents



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

11/12/2002




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.9

Shareholders Agreement between
    Shinko Electric Co., Ltd. and Asyst Japan Inc., dated as of
    May 24, 2002.


10-Q



10
.39

000-22430

11/12/200210
.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.













X10
.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.













X10
.23*

Certificate of Amendment to Option
    Grants dated August 18, 2004.


10-Q



10
.52

000-22430

12/30/2004




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.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

6/29/200510
.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).













X10
.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.













X10
.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.













X10
.39*

Separation Agreement and Release
    of All Claims between the Company and Warren C. Kocmond, dated
    May 31, 2006.













X




---



##### Table of Contents



Exhibit



Incorporated by Reference



FiledNumber

Exhibit Description

Form

Ex. No.

File No.

Filing Date

Herewith10
.40*

Change-in-Control
    Agreement between the Company and Steve Debenham, dated
    May 22, 2006.













X10
.41*

Change-in-Control
    Agreement between the Company and Alan S. Lowe, dated
    May 22, 2006.













X10
.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.













X21
.1

Subsidiaries of Asyst
    Technologies, Inc.













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).













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