Exhibit 31.1

AMTECH SYSTEMS, INC. AND ITS
SUBSIDIARIESCERTIFICATION PURSUANT TO RULE 13a-14(a)/15d-14(a)OF THE
SECURITIES EXCHANGE ACT OF 1934, AS AMENDED

I, Jong S. Whang, certify
that:

1. I have reviewed this Annual Report
on Form 10-K of Amtech Systems, Inc. (the registrant);

2. Based on my knowledge, this report
does not contain any untrue statement of a material fact or omit to state a
material fact necessary to make the statements made, in light of the
circumstances under which such statements were made, not misleading with respect
to the period covered by this report;

3. Based on my knowledge, the financial
statements, and other financial information included in this report, fairly
present in all material respects the financial condition, results of operations
and cash flows of the registrant as of, and for, the periods presented in this
report;

4. The registrants other certifying
officer and I are responsible for establishing and maintaining disclosure
controls and procedures (as defined in Exchange Act Rules 13a-15(e) and
15d-15(e)) and internal control over financial reporting (as defined in Exchange
Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) Designed such disclosure
controls and procedures, or caused such disclosure controls and procedures to be
designed under our supervision, to ensure that material information relating to
the registrant, including its consolidated subsidiaries, is made known to us by
others within those entities, particularly during the period in which this
report is being prepared;

(b) Designed such internal
control over financial reporting, or caused such internal control over financial
reporting to be designed under our supervision, to provide reasonable assurance
regarding the reliability of financial reporting and the preparation of
financial statements for external purposes in accordance with generally accepted
accounting principles;

(c) Evaluated the effectiveness
of the registrants disclosure controls and procedures and presented in this
report our conclusions about the effectiveness of the disclosure controls and
procedures, as of the end of the period covered by this report based on such
evaluation; and

(d) Disclosed in this report
any change in the registrants internal control over financial reporting that
occurred during the registrants most recent fiscal quarter (the registrants
fourth fiscal quarter in the case of an annual report) that has materially
affected, or is reasonably likely to materially affect, the registrants
internal control over financial reporting; and

5. The registrants other certifying
officer and I have disclosed, based on our most recent evaluation of internal
control over financial reporting, to the registrants auditors and the audit
committee of registrants board of directors (or persons performing the
equivalent functions):

(a) All significant
deficiencies and material weaknesses in the design or operation of internal
control over financial reporting which are reasonably likely to adversely affect
the registrants ability to record, process, summarize and report financial
information; and

(b) Any fraud, whether or not
material, that involves management or other employees who have a significant
role in the registrants internal control over financial reporting.

| | By | /s/ Jong S.
      Whang                    
| | -- | -------------------------------------------
| |    | Jong S. Whang                              
| |    | President and Chief
      Executive Officer
| |    | Amtech Systems,
    Inc.                   
| |    | Date: November 24,
      2009              

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