UNITED STATES SECURITIES AND EXCHANGE
COMMISSIONWASHINGTON, D.C. 20549 ___________ FORM
10-K/AAmendment No.
1___________

|(Mark One) |  |                                                                                                   
|---------- |  | --------------------------------------------------------------------------------------------------
|[X]        |  | ANNUAL REPORT PURSUANT TO
      SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF
    1934    
|           |  | For the fiscal year ended:
      September 30, 2008                                               
|           |  | OR                                                                                                
|[  
    ]  |  | TRANSITION REPORT PURSUANT TO
      SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF
    1934
|           |  | **For the transition period
      from ________________
  to ________________**                   

Commission File Number:0-11412

|AMTECH SYSTEMS, INC.                                                 
|---------------------------------------------------------------------
|(Exact name of registrant as
      specified in its charter)         
|                                                                     
|Arizona                                                              
|(State or
      other jurisdiction ofincorporation or organization)  
|                                                                     
|131 South Clark Drive, Tempe,
      Arizona                          
|(Address of
      principal executive offices)                       
|                                                                     
|Registrants telephone number,
      including area code:480-967-5146
|                                                                     
|Securities registered pursuant to
      Section 12(b) of the Act:None
|                                                                     
|Securities registered pursuant to
      Section 12(g) of the Act:    
|                                                                     
|Common Stock, $0.01 Par Value                                        
|(Title of Class)                                                     

Indicate
by check mark if the registrant is a well-known seasoned issuer, as defined in
Rule 405 of the Securities Act. Yes [   ] No [X]

Indicate by check mark if the
registrant is not required to file reports pursuant to Section 13 or 15(d) of
the Act. Yes [   ] No [X]

Indicate by check mark whether the
registrant (1) has filed all reports required to be filed by Section 13 or 15(d)
of the Securities Exchange Act of 1934 during the preceding 12 months (or for
such shorter period that the registrant was required to file such reports), and
(2) has been subject to such filing requirements for the past 90 days. [X] Yes
[   ] No

Indicate by check mark if disclosure
of delinquent filers pursuant to Item 405 of Regulation S-K (§ 229.405) is not
contained herein, and will not be contained, to the best of registrants
knowledge in definitive proxy or information statements incorporated by
reference in Part III of this Form 10-K or any amendment to this Form 10-K.
[X]

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Indicate
by check mark whether the registrant is a large accelerated filer, an
accelerated filer, a non-accelerated filer, or a smaller reporting company. See
definition of large accelerated filer, accelerated filer and smaller
reporting company in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer [  
      ]
    Accelerated filer [X]Non-accelerated filer [  
      ]
    Smaller reporting company [  
      ]


Indicate by check mark whether the
registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).
Yes [   ] No [X]

As of March 31, 2008, the aggregate
market value of the voting stock held by non-affiliates of the registrant was
approximately $109,255,000, based upon the closing sales price reported by the
NASDAQ Global Market on that date.

As of December 5, 2008, the
registrant had outstanding 9,096,048 shares of Common Stock, $0.01 par value.

DOCUMENTS INCORPORATED BY REFERENCE

Portions
of the Definitive Proxy Statement related to the registrants 2008 Annual
Meeting of Shareholders, were incorporated by reference into Items 10-14 of
Part III of this Form 10-K.

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EXPLANATORY NOTE

Amtech Systems, Inc. (the Company)
filed its Annual Report on Form 10-K for the fiscal year ended September 30,
2008 (the Original Filing) on December 10, 2008. Exhibits 31.1 and 31.2 to the
Original Filing contained certifications pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002 (the Certifications). The Certifications contained
certain inadvertent omissions of the certification language prescribed by Item
601(b)(31)(i) of Regulation S-K. New certifications pursuant to Section 302 of
the Sarbanes-Oxley Act of 2002 add the inadvertently omitted language and are
included as exhibits 31.1 and 31.2 to this Amendment No. 1 to Form 10-K (the
Amendment).

There is no other change made to the
Original Filing except the replacement of the Certifications as described above.
This Amendment makes no attempt to reflect events occurring after the filing of
the Original Filing and does not change any previously reported financial
results of operations or any disclosures contained in that document.

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SIGNATURES

Pursuant
to the requirements of Section 13 or 15(d) of the Securities Exchange Act of
1934, the registrant has duly caused this Amendment No. 1 to Report on Form
10-K/A to be signed on its behalf by the undersigned, thereunto duly
authorized.

|                         |     | AMTECH SYSTEMS,
      INC.                 
|------------------------ | --- | -------------------------------------------
|                        
|                        
|Date: June 5,
      2009 | By: | /s/ Bradley
      C. Anderson              
|                         |     | Bradley C.
      Anderson, Vice President -
|                         |     | Finance and
      Chief Financial Officer  

INDEX TO EXHIBITS

The following exhibits are filed
with this Report.

|Number |  | Description                                                                                                                                                                     
|------ |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|31.1   |  | Certification of the Companys Chief Executive Officer pursuant to
      18 U.S.C. Section 1350, as adopted pursuant to Section 302 of the
      Sarbanes-Oxley Act of 2002. (*)
|31.2   |  | Certification of the Companys Chief Financial Officer pursuant to
      18 U.S.C. Section 1350, as adopted pursuant to Section 302 of the
      Sarbanes-Oxley Act of 2002. (*)

* Filed herewith.

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