UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                   FORM 10-K/A
                                 AMENDMENT 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, 1999

                                       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                                           86-0411215
   -------------------------------                           -------------------
   (State or other jurisdiction of                            (I.R.S. Employer
    incorporation or organization)                           Identification No.)


 131 South Clark Drive, Tempe, Arizona                              85281
----------------------------------------                          ----------
(Address of Principal Executive Offices)                          (Zip Code)

Registrant's telephone number, including area code: 602-967-5146

The undersigned registrant hereby amends its Form 10-K for the fiscal year ended
September 30, 1999, as follows:

     Part III, Items 9-12 are hereby amended as follows:
<PAGE>
                                    PART III

ITEM 9. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT; COMPLIANCE WITH
        SECTION 16(a) OF THE EXCHANGE ACT

INFORMATION CONCERNING DIRECTORS AND OFFICERS

     The  following  table  sets  forth  information   regarding  the  officers,
directors and director nominees of the Company,  including biographical data for
at least the last five years.

     Name                 Age   Position with the Company
     ----                 ---   -------------------------
     Jong S. Whang        54    President, Chief Executive Officer and Director
     Robert T. Hass       49    Vice President-Finance, Chief Financial Officer,
                                Treasurer, Secretary and Director
     Donald F. Johnston   73    Director
     Alvin Katz           70    Director
     Bruce R. Thaw        47    Director

     JONG S. WHANG has been President, Chief Executive Officer and a Director of
the  Company  since  its  inception  and was one of its  founders.  Mr.  Whang's
responsibilities  as  President  include  the  sales  effort  for the  Company's
semiconductor  equipment  business and  development of new products and business
opportunities  in that industry.  He has  twenty-six  years of experience in the
semiconductor   industry,   including   time  spent  in  both   processing   and
manufacturing of equipment components and systems.  From 1973 until 1979, he was
employed by Siltronics,  Inc.,  initially as a technician  working with chemical
vapor deposition (CVD) and later as manager of the quartz fabrication plant with
responsibility of providing technical  marketing support.  From 1979 until 1981,
he was employed by U.S. Quartz,  Inc. as manufacturing  manager. In 1981 he left
U.S. Quartz to found the Company.

     ROBERT T. HASS has been Vice  President-Finance,  Chief Financial  Officer,
Treasurer and  Secretary of the Company since June 3, 1992.  Mr. Hass has served
as a Director of the Company since February 29, 1996.  From 1991 until May 1992,
he operated a financial  consulting  practice  under the name of Hass  Financial
Consulting Services,  a sole proprietorship.  From 1985 to 1991, Mr. Hass served
as Director of Accounting  Services and then  Controller for  Lifeshares  Group,
Inc., a holding  company  which owned and operated real estate  development  and
insurance  subsidiaries,  and from 1988 to 1991 served as  Controller  and Chief
Accounting Officer of some of those  subsidiaries.  From 1984 to 1985, he served
as Vice  President-Finance  and Treasurer of The Victorio  Company,  a privately
owned holding company which owned and operated agriculture, chemical, commercial
real estate  brokerage,  marketing  research and commodities  futures  brokerage
businesses.  From 1977 to 1984, he was employed in various capacities  including
Vice President,  Chief Financial  Officer and Treasurer by Altamil  Corporation,
then  a  public  company,   which  manufactures   truck  equipment,   wire-bound
containers,  and precision aluminum forgings. From 1972 to 1977, he was employed
as an auditor with Ernst & Ernst,  now known as Ernst & Young. He is a Certified
Public Accountant.

     DONALD F.  JOHNSTON has been a Director of the Company since April 9, 1994,
and also  served as a  Director  from  March 1983 to  December  1992.  He is not
otherwise  employed  by the  Company.  From  1985 to March  1993,  he  served as
President  and Chief  Executive  Officer of JAI,  Inc., a  management-consulting
firm.  From 1985 to March  1993,  when he  retired,  he acted as  marketing  and
management  consultant to companies in the electronics  industry.  From November
1983 until October 1985,  he was  President of Process  Control,  Inc. of Tempe,
Arizona. He has held senior management  positions with Montgomery Ward & Co. and

                                        2
<PAGE>
the Hotpoint Division of the General Electric Company. He has also served as the
Vice-President of B.F. Goodrich,  Vice-President of Marketing of the Philco Ford
Division of the Ford Motor  Company and  Executive  Vice-President  of CTV.  Mr.
Johnston  also  served  as  President  and  Chief  Executive  Officer  of  Mirco
Electronics, Amstar Electronics and Hera Investment Co.

     ALVIN  KATZ has been a Director  of the  Company  since May 1, 1995.  Since
1981,  he has been an adjunct  professor of business  management  at the Florida
Atlantic University in Boca Raton, Florida. From 1991 until the company was sold
in September 1992, he was Chief Executive Officer of Odessa Engineering Corp., a
company engaged in the manufacture of pollution monitoring equipment.  From 1957
to 1976,  Mr.  Katz was  employed  by  United  Parcel  Service  holding  various
managerial  positions,  including  District  Manager  and  Corporate  Manager of
Operations Planning,  Research and Development. He is also a Director of Blimpie
International,  a fast food franchiser,  Nastech Pharmaceutical Company, Inc., a
company  engaged in research,  development  and  marketing of nasally  delivered
pharmaceuticals,  and President of BMAC, a biomedical automation company, all of
which are publicly held corporations.

     BRUCE R. THAW has been a Director  of the  Company  since May 1, 1995.  Mr.
Thaw has been a practicing  attorney since 1978. Since 1995, Mr. Thaw has been a
self-employed  attorney, and from 1984 to 1995, he was a partner in the law firm
of  Abrams  &  Thaw.  Mr.  Thaw  is  also a  Director  of  Information  Resource
Engineering,  Inc., a publicly  traded  company that designs,  manufactures  and
markets   computer   network   security   systems  and  products,   and  Nastech
Pharmaceutical Company, Inc., a publicly traded company engaged in the research,
marketing and development of pharmaceutical  products.  Mr. Thaw does not render
legal services to the Company.

COMPLIANCE WITH SECTION 16(a) OF THE SECURITIES EXCHANGE ACT OF 1934

     Section 16(a) of the Securities Exchange Act of 1934, as amended,  requires
the Company's directors and executive officers,  as well as persons beneficially
owning more than 10% of the Company's  outstanding Common Stock, to file certain
reports of ownership  with the Securities  and Exchange  Commission  (the "SEC")
within  specified time periods.  Such officers,  directors and  shareholders are
also  required by SEC rules to furnish  the  Company  with copies of all Section
16(a) forms they file.

     Based  solely  on its  review of such  forms  received  by it,  or  written
representations  from  certain  reporting  persons,  the Company  believes  that
between  October  1,  1998 and  September  30,  1999 all  Section  16(a)  filing
requirements  applicable to its officers,  directors and 10%  shareholders  were
complied  with,  except that  reports  were not timely filed with respect to the
automatic  option grant to directors  arising under the  Company's  Non-employee
Directors Stock Option Plan and the options grants reflected in Item 10 below.

ITEM 10. EXECUTIVE COMPENSATION

     The  following  table sets  forth  annual and  long-term  compensation  for
services in all  capacities to the Company for the fiscal years ended  September
30, 1999, 1998 and 1997 of the Company's Chief Executive Officer,  and the other
most highly  compensated  executive  officer of the Company who received  annual
compensation  exceeding  $100,000  during such  periods  (the  "Named  Executive
Officers").

                                        3
<PAGE>
                           SUMMARY COMPENSATION TABLE

<TABLE>
<CAPTION>
                                                                         Long-Term
                                        Annual Compensation             Compensation
                               --------------------------------------   ------------
     Name and        Fiscal                            Other Annual      Restricted      All Other
Principal Position    Year     Salary    Bonus(1)     Compensation(2)   Stock Awards   Compensation(3)
------------------    ----     ------    --------     ---------------   ------------   ---------------
<S>                   <C>    <C>         <C>               <C>              <C>            <C>
Jong S. Whang         1999   $ 130,200   $ 12,292           --               --            $    0
President and Chief   1998     167,147          0           --               --             3,037
Executive Officer     1997     139,615     33,994(1)        --               --             3,693

Robert T. Hass        1999      85,500          0           --               --                 0
Vice President-       1998      96,105      7,245           --               --             2,123
Finance               1997      89,838     10,771           --               --             1,935
</TABLE>

----------
(1)  On  February  24,  1989,  the  Board of  Directors  approved  an  incentive
     compensation  plan for Mr. Whang,  which  provides for an annual cash bonus
     equal  to 2% of  the  annual  profits  of  the  Company  before  taxes  and
     extraordinary  items;  plus 2% of the amount by which the  revenues  of the
     Company's  semiconductor  equipment  business  in  each  year  exceed  such
     revenues  for the  previous  year.  It is a condition to the payment of any
     bonus that Mr. Whang have been continually employed by the Company and that
     the  Company  have  realized a profit  after the  payment of the bonus.  On
     February 28, 1997,  Mr. Whang entered into an employment  contract with the
     Company,  which contract  incorporated Mr. Whang's  incentive  compensation
     plan and added  additional  bonus  eligibility  criteria.  See  "Employment
     Contracts with Executive  Officers," below.  Effective October 4, 1998, Mr.
     Whang voluntarily initiated a 20% reduction in his salary to $130,200.

(2)  Other  compensation to Messrs.  Whang and Hass,  consisting of the use of a
     Company car, vacation pay and other perquisites,  did not exceed $50,000 or
     10% of base compensation during any fiscal year covered by this table.

(3)  Amounts for Mr. Whang include annual insurance  premiums paid on whole-life
     insurance for the benefit of Mr.  Whang's spouse of $225 in fiscal 1997 and
     Company matching contributions in the Amtech Systems, Inc. 401(k) Plan (the
     "Amtech 401(k) Plan") for Mr. Whang of $0, $3,037 and $3,438 in 1999,  1998
     and 1997,  respectively.  Amounts for Mr. Hass represent  Company  matching
     contributions  in the Amtech 401(k) Plan.  Effective  October 4, 1998,  Mr.
     Hass' annual salary was reduced to $85,500.

                                        4
<PAGE>
OPTION GRANTS

     The table  shown  below  contains  information  on grants of stock  options
during the 1999 fiscal year to the Named Executive Officers.

                       OPTIONS GRANTS IN LAST FISCAL YEAR

<TABLE>
<CAPTION>
                                    Individual Grants
                           --------------------------------------             Potential Realizable Value
               Securities    % of Total                  Stock                at Assumed Annual Rates of
               Underlying      Options                  Price on               Stock Price Appreciation
                Options      Granted to      Exercise    Date of                 for Option Term(4)
                Granted      Employees        Price       Grant    Expiration  -------------------------
      Name        (#)      in Fiscal 1999   ($/Share)   ($/Share)     Date       0%       5%       10%
      ----      -------    --------------   ---------   ---------     ----     ------   ------    ------
<S>             <C>             <C>          <C>          <C>       <C>         <C>     <C>       <C>
Jong S. Whang   2,500(1)         8%          $1.50(3)     $1.50     10/01/08     -0-    $2,358    $5,977
Robert T. Hass  5,000(2)        15%          $1.13(3)     $1.13      2/26/09     -0-    $3,541    $8,973
</TABLE>

----------
(1)  All  options  were  granted to Mr.  Whang on  February  26,  1999 under the
     applicable  Stock Option Plan. The options  granted  become  exercisable as
     follows:  20% on February 26, 2000,  and an additional 20% on each one year
     anniversary thereafter. To the extent not already exercisable,  the options
     become immediately  exercisable upon: (i) the dissolution or liquidation of
     the Company or a  reorganization,  merger or  consolidation in which all or
     substantially  all prior  shareholders do not continue to own more than 60%
     of the outstanding shares of common stock and voting  securities;  (ii) the
     sale of all or substantially all of the assets of the Company; or (iii) the
     occurrence of a change in control of the Company.

(2)  All  options  were  granted  to Mr.  Hass on  October  1,  1998  under  the
     applicable  Stock Option Plan. The options  granted  become  exercisable as
     follows:  20% on  October  1, 1999 and an  additional  20% on each one year
     anniversary thereafter.

(3)  The exercise price was set at 100% of closing price of the Company's Common
     Stock on grant day, (February 26, 1999 for options granted to Mr. Whang and
     October 1, 1998 for options granted to Mr. Hass), as reported on the NASDAQ
     SmallCap Market.  The options granted to Mr. Hass were re-priced on October
     14,  1998,  along with all other  outstanding  stock  options to the market
     price on that date, ($1.126).

(4)  Reflects  the value of the stock  option on the date of grant  assuming (i)
     for the 0% column,  no  appreciation  in the Company's stock price from the
     date of grant over the term of the option,  (ii) for the 5% column,  a five
     percent annual rate of  appreciation  in the Company's stock price over the
     term of the option, and (iii) for the 10% column, a ten percent annual rate
     of  appreciation  in the Company's stock price over the term of the option,
     in each case without any discounting to present value. The actual gains, if
     any, on stock option exercises are dependent upon the future performance of
     the Company's  Common  Stock.  Accordingly,  the amounts  reflected in this
     table may not necessarily be indicative of the actual results obtained.

OPTION EXERCISES

     There were no exercises  of stock  options  during  fiscal year 1999 by the
Named Executive Officers.

                                        5
<PAGE>
BOARD REPORT ON REPRICING

     The Board believes that the Company has taken constructive steps to improve
its  performance and believes that hiring and retaining key employees is central
to implementing these measures.  In furtherance of these goals, in October 1998,
the Board reduced the per share exercise price of options  previously granted to
Jong S. Whang and Robert T. Hass. The Board concluded that the results  achieved
by these executives were the basis for the repricing of options granted to them.
No other provisions of these options were altered.

     In  accordance  with the rules of the  Securities  and Exchange  Commission
("SEC"),  this Option Repricing Report of the Board of Directors is not intended
to be "filed" or "soliciting  material" or subject to Regulations  14A or 14C or
Section 18 of the Securities Exchange Act 1934, as amended, or incorporated into
any other filing by the Company with the SEC.

AMENDMENT OR RE-PRICING OPTIONS

     The table below  setsforth  information  for all  executive  officers  with
respect to re-pricing of options for the 10 years preceding September 30, 1999.

                        Ten Year Option/SAR Repricings(1)

<TABLE>
<CAPTION>
                                 Number of                                               Length of
                                 Securities    Market Price    Exercise               Original Option
                                 Underlying     of Stock at    Price of               Term Remaining
                                  Options        Time of     Stock at Time    New       at Date of
                                 Repriced or   Repricing or  or Repricing   Exercise   Repricing or
     Name               Date      Amended       Amendment    or Amendment    Price       Amendment
     ----               ----      -------       ---------     ---------      -----       ---------
<S>                <C>             <C>           <C>            <C>         <C>        <C>
Jong S. Whang      Oct. 14, 1998   103,792        $1.126         $5.00       $1.126     8 3/8 years
President and CEO
Robert T. Hass     Oct. 14, 1998     1,250        $1.126         $5.00       $1.126     8 3/8 years
VP-Finance         Oct. 14, 1998     5,000        $1.126         $1.50       $1.126        10 years
</TABLE>

----------
(1)  The number of shares and the  prices  per share have all been  restated  to
     give effect for the two-for-one reverse split that took effect on March 15,
     1999.

EMPLOYMENT CONTRACTS WITH EXECUTIVE OFFICERS

     On February 28, 1997, the Company  entered into a five (5) year  employment
agreement with its President,  Jong S. Whang.  Under the terms of the agreement,
Mr. Whang is entitled to an annual  salary of $170,900 on October 1, 1998,  with
annual  increases of at least 5% to be  determined  by the Board of Directors at
the end of each year of the  agreement.  Effective  October 4, 1998,  Mr.  Whang
voluntarily initiated a 20% reduction in his salary to $130,200. In addition, he
is entitled to receive annual  incentive cash  compensation  of up to 50% of his
base salary, to be calculated as follows:  (i) a bonus equal to 2% of the annual
earnings of the Company before taxes and  extraordinary  items, and (ii) a bonus
equal to 2% of the amount by which the revenues of the  Company's  semiconductor
equipment  business in each year exceeds such revenues for the previous year. It
is a condition  to the payment of any cash bonus that Mr.  Whang shall have been
continuously  employed  by the  Company and that the total of all cash and stock
bonuses is  limited  to 10% of the  Company's  pre-tax  earnings  for that year.
Profits are determined without taking into account the first $3,200,000 expended
or invested by the Company in the development of the proposed photo-assisted CVD
product,  which has been suspended.  In addition,  Mr. Whang was granted 103,792

                                        6
<PAGE>
stock options pursuant to the agreement.  These options were granted on February
28,  1997 and vest at the rate of 20% per full year of service  over a five-year
period. To the extent not already  exercisable,  the options become  immediately
exercisable  upon:  (i) the  dissolution  or  liquidation  of the  Company  or a
reorganization,  merger or consolidation in which all or substantially all prior
shareholders do not continue to own more than 60% of the then outstanding shares
of Common Stock and voting securities, (ii) the sale of all or substantially all
of the assets of the Company,  or (iii) the occurrence of a change in control of
the  Company  as  discussed  in  the  agreement.  The  agreement  also  contains
confidentiality  and non-compete  provisions.  If Mr. Whang is terminated  other
than for "cause," he is entitled to receive as severance  pay salary,  incentive
compensation  and  vacation  accrued  through the date of  termination  plus the
greater of his then annual salary or the balance of his  compensation to the end
of the term of the employment  agreement  computed  using the latest  applicable
salary rate without  consideration of any salary  reductions.  Mr. Whang is also
entitled to participate in any benefit plans generally available to employees of
the Company.

COMPENSATION AND OPTION COMMITTEE REPORT ON EXECUTIVE COMPENSATION

     The  Compensation  and Option Committee of the Company's Board of Directors
(the "Committee), which is composed entirely of independent,  outside directors,
establishes  the general  compensation  policies  of the  Company  and  specific
compensation  for each executive  officer of the Company,  and  administers  the
Company's  stock  option  program.   The  Committee's  intent  is  to  make  the
compensation  packages of the  executive  officers of the Company  sufficient to
attract and retain  persons of  exceptional  quality,  and to provide  effective
incentives to motivate and reward Company executives for achieving the financial
and strategic goals of the Company essential to the Company's  long-term success
and to growth in shareholder value. The Company's executive compensation package
consists of three main components:  (1) base salary, (2) incentive cash bonuses,
and (3) stock options.

ITEM 11. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

SECURITY OWNERSHIP OF MANAGEMENT

     The  following  table  sets  forth  certain   information   concerning  the
beneficial  ownership of the  Company's  Common Stock as of January 21, 2000, by
(i) each director and each nominee for director of the Company,  (ii) certain of
the Company's executive officers (the "Named Executive Officers"), and (iii) all
executive  officers and directors as a group.  There are no persons known to the
Company  who  beneficially  own  five  percent  (5%) or  more  of the  Company's
outstanding  Common Stock.  This  information  was determined in accordance with
Rule 13d-3 under the Securities  Exchange Act of 1934, as amended,  and is based
upon the information  furnished by the persons listed below. Except as otherwise
indicated,  each  shareholder  listed possesses sole voting and investment power
with respect to the shares indicated as being beneficially owned.

                                        7
<PAGE>
                                           Number of Shares          Percent of
      Name and Address(1)(2)             Beneficially Held(3)       Ownership(3)
      ----------------------             --------------------       ------------
Jong S. Whang                                 114,463(4)                5.3%
Robert T. Hass                                  8,250(5)                 *
Donald F. Johnston                             10,625(6)                 *
Alvin Katz                                     87,500(6)                4.1%
Bruce R. Thaw                                  21,500(6)                1.0%
Directors and Executive Officers of
 the Company as a group (5 persons)           242,338(7)               11.5%

----------
* Less than 1%.

(1)  The  address for each  person  listed in this table is c/o Amtech  Systems,
     Inc., 131 South Clark Drive, Tempe, Arizona 85281.

(2)  Mr. Whang is the Company's President,  CEO and a director.  Mr. Hass is the
     Vice President-Finance, Chief Financial Officer, Treasurer, Secretary and a
     director. Messrs. Johnston, Katz and Thaw are presently directors.

(3)  The  shares  and  percentages  shown  include  the  shares of Common  Stock
     actually  owned as of January 17, 2000, and the shares of Common Stock with
     respect to which the person had the right to acquire  beneficial  ownership
     within 60 days of such date pursuant to options or warrants.  All shares of
     Common Stock that the identified  person had the right to acquire within 60
     days of January  21,  2000 upon the  exercise  of options or  warrants  are
     deemed to be  outstanding  when  computing the percentage of the securities
     owned by such person,  but are not deemed to be outstanding  when computing
     the percentage of the securities owned by any other person.

(4)  Includes (i) 9,488 shares held  jointly  with Mr.  Whang's  spouse and (ii)
     62,775 shares issuable upon the exercise of presently  exercisable options;
     62,275  shares  issuable  at an  exercise  price of $1.126 per  share;  the
     balance of 500 shares issuable at an exercise price of $1.50 per share.

(5)  Includes  1,750 shares  issuable  upon  exercise of  presently  exercisable
     options with an exercise price of $1.126 per share.

(6)  Includes  10,000 shares  issuable  upon  exercise of presently  exercisable
     options;  9000 shares issuable at an exercise price of $1.126 per share and
     the  balance of 1000  shares  issuable  at an  exercise  price of $1.50 per
     share.

(7)  Includes  94,525 shares  issuable  upon  exercise of presently  exercisable
     options;  91,025 shares  issuable at an exercise  price of $1.126 per share
     and the balance of 3,500 shares  issuable at an exercise price of $1.50 per
     share.

ITEM 12. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

     The  Company  did not have any  transactions  during  fiscal  1999 with any
director,  director  nominee,  executive  officer,  security holder known to the
Company to own of record or  beneficially  more than 5% of the Company's  Common
Stock, or any member of the immediate family of any of the foregoing persons, in
which the amount involved exceeded $60,000.

                                        8
<PAGE>
                                   SIGNATURES


Pursuant to the requirements of Section 13 or 15 (d) of the Securities  Exchange
Act of 1934,  the  Registrant  has duly  caused  this report to be signed on its
behalf by the undersigned, thereunto duly authorized.

                                        AMTECH SYSTEMS, INC.

February 28, 2000                       By /s/  Jong S. Whang
                                           -------------------------------------
                                           Jong S. Whang, President

Pursuant  to the  requirements  of the  Securities  Exchange  Act of 1934,  this
Amendment No. 1 to Form 10-K has been signed below by the  following  persons on
behalf of the registrant and in the capacities and on the dates indicated:

       Signature                     Title                           Date
       ---------                     -----                           ----

/s/ Jong S. Whang           Chairman of the Board, President   February 28, 2000
-------------------------   (Chief Executive Officer)
Jong S. Whang


/s/ Robert T. Hass          Vice President-Finance             February 28, 2000
-------------------------   (Chief Financial & Accounting
Robert T. Hass              Officer)


/s/ *                       Director                           February 28, 2000
-------------------------
Donald F. Johnson


/s/ *                       Director                           February 28, 2000
-------------------------
Alvan Katz


/s/ *                       Director                           February 28, 2000
-------------------------
Bruce R. Thaw


*By: /s/ Jong S. Whang                                         February 28, 2000
     ----------------------------
     Jong S. Whang

                                        9