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May 18, 2009

Brian Cascio, Branch Chief
Division
of Corporation Finance
United States
Securities and Exchange Commission
100 F Street, N.E.
Washington, D.C. 20549

    Re:

    Amtech Systems, Inc.

    Form
      10-K for the fiscal year ended September 30, 2008

    Filed
      December 10, 2008

    File
      No. 000-11412

Dear Mr. Cascio:

This letter sets forth the responses of
Amtech Systems, Inc. (the "Company") to your comment letter, dated March 31,
2009, relating to (i) the Form 10-K for the fiscal year ended September 30, 2008
of the Company filed with the Securities and Exchange Commission (the
"Commission") on December 10, 2008; (ii) the Form 10-Q for the quarter ended
December 31, 2008, filed with the commission on February 9, 2009; and (iii) the
current report on Form 8-K/A filed with the Commission on November 2, 2007.

The Company is filing, via EDGAR, this
letter setting forth the Company's responses to comments of the Staff of the
Commission (the "Staff"). Enclosed as well are two hard copies of the Company's
response letter. We have included your original questions in addition to
providing our responses.

Form 10-K for the fiscal year ended
September 30, 2008

Item 1. Business, page
3

    1.

      We note your disclosure on page 4
      that in “fiscal 2008, [y]our net revenue” and that [y]our top 10 customers
      collectively represented approximately 62% of [y]our net
      revenue:

      Additionally, we note your
      disclosure on page 14 that in “fiscal 2008, 2007 and 2006, one customer
      accounted for approximately 20%, 13% and 17% of [y]our net revenue,
      respectively.” Please tell us, and in future filings disclose, the name of
      the customer, which we note “has been different [each year],” and any
      relationship with that customer, pursuant to the requirements of
      Regulation S-K Item 101(c)(vii). Please also tell us which customers
      accounted for the 22% and 20% of total accounts receivable at September
      30, 2008.

    131 South Clark Dr. Tempe, AZ
      85281
    Tel: (480) 967-5146  Fax: (480)
      968-3763

Brian Cascio, Branch Chief
Division
of Corporation Finance
United States
Securities and Exchange Commission
May 18, 2009
Page 2 of 12

    R:

      According to Regulation S-K §
      229.101(c)(vii) disclosure of the name of the customer and its
      relationship, if any, is required “if sales to the customer…equal to 10
      percent or more of the registrant’s consolidated revenues and the loss of
      such customer would have a material adverse effect on the registrant and
      subsidiaries taken as a whole.” As you have noted, we disclosed that our
      largest customer has been different in each of the last three years. The
      ranking of our largest customers, most of whom represent less than 10% of
      consolidated revenue, varies significantly from year to year. Our
      products/systems are designed to operate for many years; thus, significant
      sales to the same customers in consecutive years generally do not occur.
      Since we do not rely on the same 10% or more customers for recurring
      revenue of a similar magnitude, we do not believe that the loss of any one
      of these customers would have a material adverse effect on future
      operations or the financial condition of the Company. This was borne out
      in the six months ended March 31, 2009, during which the 20% customer in
      fiscal 2008 represented 2% of consolidated revenue and ranked
      13th based on revenue during the six months ended March 31,
      2009. In future filings, we will disclose the names of 10% or more
      customers if the conditions set forth in the regulations are
      met.

      The registrant had no other
      relationship with the referenced customers.

      Though, for the reasons mentioned
      above we do not believe disclosure of customer names is material or
      required, in order to ensure compliance with your request number 1, we are
      providing that information here. The customers that accounted for
      approximately 20%, 13%, and 17% of net revenue in fiscal 2008, 2007, and
      2006 were Yingli Green Energy Holding Company Ltd. (NYSE: YGE), E-ton
      Solar Tech. Co., Ltd, and Infineon AG. The customers that accounted for
      the 22% and 20% of total accounts receivable at September 30, 2008 were
      Tianwei New Energy Holdings Co. Ltd. and Yingli Green Energy Holding
      Company Ltd. (NYSE: YGE), respectively.

Brian Cascio, Branch Chief
Division
of Corporation Finance
United States
Securities and Exchange Commission
May 18, 2009
Page 3 of 12

Item 11. Executive
Compensation

To facilitate your review, we have
included text from our proxy, or references to our proxy, in our responses to questions
relating to Item 11 of the 10-K for the fiscal year ended September 30, 2008.

Determining Executive Compensation,
page 7

    2.

      We note your disclosure that your
      compensation committee considers “compensation of executives of comparable
      companies within similar industries” when making salary recommendations
      for your named executive officers. Since you appear to benchmark
      compensation, please discuss how each element of compensation relates to
      the data you analyzed from peer companies and include an analysis of where
      actual payments actually fell within the targeted parameters. If any of
      your named executive officers are compensated at levels that are
      materially different from the targeted levels of compensation, please also
      provide discussion and analysis as to why. In addition, in your applicable
      future filings, please identify the peer companies that you use. See
      Regulations S-K Item 402(b)(2)(xiv).

    R:

      As noted on page 7 of our Proxy
      Statement, “our Compensation Committee reviews information regarding
      salaries, including the compensation of comparable companies within
      similar industries and to make recommendations regarding the salary of our
      chief executive office and chief financial officer.” As it relates
      specifically to base or salary compensation, page 8 of our Proxy Statement
      states the following: “During fiscal 2008, our chief financial officer, at
      the request of our Compensation Committee, summarized the base pay for
      chief executive officers and chief financial officers as reported in the
      American Electronics Association Salary Survey. Using parameters that best
      fit our company (for example, revenues, public companies, similarities in
      numbers of employees, and geographic region), our chief financial officer
      presented a statistical summary of such information and made
      recommendations to our Compensation Committee that were in line with the
      average and median salaries of similarly situated
  companies.”

      The reference to “comparable
      companies” found on page 7 was in the context of an overall review of
      compensation and the specific data from the survey discussed on page 8 was
      the primary data used by the Compensation Committee in determining base
      compensation for the chief executive officer and chief financial officer.
      Based on the survey analysis reviewed by the compensation committee, the
      average of the median base salary for the positions of CEO and
      CFO was $280,000 and $202,000, respectively. The salary approved by the
      compensation committee for the CEO and CFO was $275,000 and $198,000,
      respectively.

Brian Cascio, Branch Chief
Division of Corporation Finance
United States Securities and Exchange Commission
May 18,
2009
Page 4 of 12

    3.

      We also note your disclosure here and on
      page 8 that you rely upon “published and proprietary survey data” when
      implementing your compensation programs. Please identify the surveys you
      used and their components; include component companies, the elements of
      compensation that are benchmarked and how you determine such
      benchmarks.

    R:

      Page 8 of our Proxy Statement states the
      following (emphasis added): “During fiscal 2008, our chief financial officer, at the
      request of our Compensation Committee, summarized the base pay for chief
      executive officers and chief financial officers as reported in the
      American Electronics Association Salary
      Survey. That
      survey benchmarks base salary, bonus and other unspecified
      compensation.  Since cash incentive compensation for our named
      executives is calculated under our bonus program based upon quantifiable
      measures of performance, we limited our use of the survey to base salary.
      Using parameters that best fit our company (for example, revenues, public companies, similarities in numbers of employees, and geographic region), our chief financial
      officer presented a statistical summary of such information and made
      recommendations to our Compensation Committee that were in line with the
      average of the median salaries of similarly situated
  companies.”

      The survey data did not provide a separate
      listing of the individual companies included within the data, but was
      based upon companies that are in or serve the electronics industries,
      which includes manufacturers of equipment used by semiconductor and solar
      cell manufacturers.  The survey does not include specific data for
      equity based compensation.

Elements of Our Executive
Compensation Program, page 8

    4.

      You state that the compensation committee
      considers “the roles and responsibilities” and “the individual experience
      and skills of [y]our executives” when making compensation decisions.
      Please provide additional disclosure to discuss and analyze how individual
      performance contributes to actual compensation for named executive
      officers. For example, disclose the elements of individual performance,
      both quantitative and qualitative, and specific contributions by named
      executive officers that the compensation committee considers in its
      evaluation. If applicable, please also discuss how these elements are
      weighted and factored into specific compensating decisions. See
      Regulations S-K 402(b)(2)(vii).

    R:

      The compensation committee primarily
      considers the roles, responsibilities, skills and experience of the named
      executives in establishing base salary. Our chief executive
      officer is also one of the founders of the company and has over 30 years
      of experience in the markets in which we serve. In addition to his CEO
      role, he effectively serves as our chief sales and marketing officer, and
      chief strategy officer, although we do not have those specific executive
      positions. In these roles, our CEO provides leadership in developing the
      Company’s sales and marketing plans and product acquisition and
      development strategies. Our chief financial officer is heavily involved in
      the operations of the company, in addition to his roles in finance,
      investor relations, SEC reporting, tax planning and compliance, budgeting
      and forecasting, and serves as a quasi chief operating officer, although
      we do not have that specific executive position. All three of our
      executives have experience in equity financings. These qualitative factors
      are some of the major items considered by the compensation committee in
      its evaluation.

      Quantitative contributions are used
      primarily in establishing the levels of cash incentive compensation for
      our names executives. As reflected in our compensation discussion and
      analysis on page 9 of our Proxy Statement, our bonus program is
      quantitatively based upon performance objectives established in each of
      the following categories: (i) bookings; (ii) revenue; (iii) gross margin;
      and (iv) operating profit.

Brian Cascio, Branch Chief
Division
of Corporation Finance
United States
Securities and Exchange Commission
May 18, 2009
Page 5 of 12

    Annual Cash Compensation, page 8

    5.

      We note that you increased base
      salary compensation for your CEO and CFO by approximately 10% and for your
      chief accounting officer by approximately 15% during fiscal year 2008.
      Tell us, and expand your disclosure in future filings to explain, what
      factors you considered in the decision to make these material increases in
      compensation. See Regulations S-K Item 402(b)(ix).

    R:

      Based on our analysis of the AEA survey, our
      compensation committee determined that the aforementioned raises were
      necessary in order to bring our executive compensation in line with that
      of the industry and ensure we retain our executive talent. Please also see
      our response to question 4 which further describes the factors considered
      in the decision to make these material increases in compensation. In
      future filings we will expand our disclosure with respect to this
      matter.

    Equity Incentive Compensation, page 9

    6.

      We believe that investors will
      benefit from an expanded analysis of how you arrived at and why you paid
      each particular level of compensation for 2008. For example, we note
      minimal discussion and analysis of how you determined specific stock
      option awards, as disclosed on pages 9 and 10. We would expect to see a
      more focused discussion that provides substantive analysis and insight
      into how the Committee made actual payout determinations for the fiscal
      year for which compensation is being reported. Refer to paragraphs
      (b)(1)(iii) and (v) of Regulation S-K Item 402. In your response and in
      future filings, please also clarify the reasons for differences in the
      relative size of the grants among the officers.

      Please understand that discussion
      of the various items of corporate and individual performance that were
      considered by you must be accompanied by a complete qualitative and
      quantitative discussion of how you determined to award each specific form
      and level of compensation. You should provide complete discussions of
      specific factors considered by the Committee in ultimately approving this
      and other forms of compensation, including the reasons why the Committee
      believed that the amounts paid to each named executive officer are
      appropriate in light of the various items it considered in making specific
      compensation decisions.

Brian Cascio, Branch Chief
Division
of Corporation Finance
United States
Securities and Exchange Commission
May 18, 2009
Page 6 of 12

    R:

      Please note that the value of stock option
      awards in fiscal 2008 represent between 7% and 17% of total compensation
      for our named executives, significantly less than the percent of total
      compensation represented by base salary or cash incentive compensation.
      See the Summary Compensation Table on page 11. As disclosed on pages 9 and
      10, the committee did not apply a rigid formula in allocating equity
      incentive compensation to our executives as a group or to any particular
      executive. Instead, the committee exercised its judgment and discretion
      and considered qualitatively a number of factors as outlined on page 10.
      There were no quantitative calculations or measurements performed on the
      qualitative factors. The primary reason for the differences in the
      relative size of the grants among the officers is the role and
      responsibility of the executive and his contribution to the overall
      success of the company. As described in response to question number 4, we
      are staffed very leanly at the execu