<PAGE>

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   ----------


                                  FORM 10-K/A



                                (Amendment No.1)


              Annual Report pursuant to Section 13 or 15(d) of the
                         Securities Exchange Act of 1934

                   FOR THE FISCAL YEAR ENDED DECEMBER 31, 2005

                           COMMISSION FILE NO. 0-18602

                                ATS MEDICAL, INC.
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                                         <C>
           MINNESOTA                                             41-1595629
(State or other jurisdiction of                               (I.R.S. Employer
 incorporation or organization)                             Identification  No.)
</TABLE>

<TABLE>
<S>                                                         <C>
        3905 ANNAPOLIS LANE NORTH
         MINNEAPOLIS, MINNESOTA                                     55447
(Address of principal executive offices)                         (Zip Code)
</TABLE>

       Registrant's telephone number, including area code: (763) 553-7736

        Securities registered pursuant to Section 12(b) of the Act: None

           Securities registered pursuant to Section 12(g) of the Act:
                           Common Stock $.01 par value

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 Section 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.

                               Yes   X   No
                                   -----    -----

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K 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
           -----
Indicate by check mark whether the registrant is a large accelerated filer, an
accelerated filer, or a non-accelerated filer. See definition of "accelerated
filer and large accelerated filer" in Rule 12b-2 of the Exchange Act (Check
one):

Large accelerated filer     Accelerated filer  X  Non-accelerated filer
                        ---                   ---                       ---

Indicate by check mark whether the registrant is a shell company (as defined in
Rule 12b-2 of the Act).

                               Yes       No   X
                                   -----    -----

The aggregate market value of voting and non-voting stock held by non-affiliates
of the registrant as of June 30, 2005, was approximately $107,457,665 (based on
the last sale price of such stock as reported by the NASDAQ National Market on
such date).


The number of shares outstanding of the registrant's common stock, $.01 par
value per share, as of April 24, 2006, was 31,223,127 shares.







Documents Incorporated by Reference: None.



                                EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A ("Form 10-K/A") to our Annual Report on Form
10-K for the fiscal year ended December 31, 2005, initially filed with the
Securities and Exchange Commission ("SEC") on March 7, 2006 (the "Original
Filing"), is being filed to include information required by Items 10, 11, 12, 13
and 14 under Part III. This information is being included in this Form 10-K/A
because our definitive proxy statement will not be filed within 120 days after
the end of our 2005 fiscal year. Reference to our proxy statement on the cover
page of this Form 10-K/A has been deleted.

In addition, pursuant to the rules of the SEC, Item 15 of Part IV of the
Original Filing has been amended to contain currently-dated certifications from
our Chief Executive Officer and Chief Financial Officer, as required by Section
302 of the Sarbanes-Oxley Act of 2002. The certifications of our Chief Executive
Officer and Chief Financial Officer are attached to this Form 10-K/A as Exhibits
31.1 and 31.2, respectively.

Except for the foregoing amended information, this Form 10-K/A continues to
describe conditions as of the date of the Original Filing, and we have not
updated the disclosures contained herein to reflect events that occurred at a
later date.

<PAGE>

                                    PART III

ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

EXECUTIVE OFFICERS

Biographical information regarding our executive officers is set forth under
Part I, Item 1 in the Original Filing.

BOARD OF DIRECTORS


Our Board of Directors is currently composed of the following five directors:



JOHN D. BUCK, 55, has served as Chief Executive Officer of Whitefish Ventures,
LLC, which provides financial services and strategic business expertise to small
companies, since 2000. Prior to Whitefish Ventures, he was President and Chief
Operating Officer at Fingerhut Companies, Inc. from 1996 to 2000 and played an
integral role in developing the business services area of the company. Prior to
Fingerhut, Mr. Buck was Vice President of Administration at Alliant Techsystems,
a leading supplier of aerospace and defense technologies. Prior to that, Mr.
Buck spent 21 years at Honeywell, Inc. where he served as Vice President of
Administration. Mr. Buck is Chairman of the Board of Directors of Medica, the
second largest health benefits plan in Minnesota, and a member of the board of
directors of ValueVision Media, Inc./Shop NBC. Mr. Buck was elected as a
Director of ATS Medical in September of 2004.


MICHAEL D. DALE, 46, has been Chief Executive Officer, President and Chairman of
the board of directors of ATS Medical since October 2002. From 2000 to 2002, Mr.
Dale was Vice President of Worldwide Sales and Marketing at Endocardial
Solutions, Inc. a company that develops, markets and distributes an advanced
cardiac mapping system. Mr. Dale joined Endocardial Solutions in December 1998
as Vice President of Worldwide Sales. From 1996 to 1998, Mr. Dale was Vice
President of Global Sales for Cyberonics, Inc., a medical device company, and
additionally was managing director of Cyberonics Europe S.A. From 1988 to 1996,
Mr. Dale served in several capacities at St. Jude Medical, most recently as the
Business Unit Director for St. Jude Medical Europe. Mr. Dale is on the board of
directors of Enpath Medical, Inc., a medical products company that designs,
develops, manufactures and markets percutaneous delivery solutions.


DAVID D. KOENTOPF, 63, has served as Chairman and Chief Executive Officer of
Command Trading Systems, LLC, a producer of high-precision toolholders and
distributer of modular boring systems throughout North America, since 1997.
Prior to Command, Mr. Koentopf was President of Lifetouch, Inc., a school and
retail photography company, for eight years and was President and Chief
Executive Officer of Steiger Tractor, Inc., a large four-wheeled tractor
manufacturer, for six years. Mr. Koentopf was appointed as a Director of ATS
Medical in July of 2005.


ROBERT E. MUNZENRIDER, 61, is a retired financial and operating executive. From
2000 to 2002, Mr. Munzenrider was President of Harmon AutoGlass, a subsidiary of
Apogee Enterprises, Inc. In 1999, he served as Vice President and Chief
Financial Officer of the Glass Services Segment of Apogee Enterprises. He also
served as Executive Vice President and Chief Financial Officer of Eliance Corp.,
an e-commerce service provider, during part of 1999. From 1997 to 1998, Mr.
Munzenrider served as Vice President and Chief Financial Officer of St. Jude
Medical, Inc. From 1983 to 1997, he served as Vice President and Chief Financial
Officer of three subsidiaries of Viad Corp. and predecessor companies, including
Travelers Express Company, Inc., Restaura, Inc. and Bell Atlantic Systems
Leasing, Int. (previously Greyhound Computer Corporation). Mr. Munzenrider is a
Certified Public Accountant. Mr. Munzenrider also serves as a director on the
boards of Viad Corp and CABG Medical, Inc., and is a Trustee on the University
of Montana Foundation. Mr. Munzenrider was elected as a director of ATS Medical
in June 2003.

ERIC W. SIVERTSON, 55, has served as the President and Chief Executive Officer
of Dymedix Corporation, which designs, manufactures and markets sensors to sleep
labs worldwide, since December 2004. Prior to Dymedix, Mr. Sivertson was a
partner in the Minneapolis office of DHR International Executive Search, which
focuses on the medical device, diagnostic and healthcare supply industries, from
2003 to 2005. From 2002 to 2003, Mr. Sivertson was a partner at TMP/Highland
Partners, an executive search firm. From 1999 to 2003, Mr. Sivertson served as
President and Chief Executive Officer of netRegulus, Inc., a web-based
regulatory and clinical information technology company. From 1997 to 1999, Mr.
Sivertson served as President and Chief Executive Officer of Biocompatible
Cardiovascular, Ltd. Preceding this, Mr. Sivertson served as Division President
of International Cardiovascular and Cardiac Rhythm Management for St. Jude
Medical, a medical device manufacturer and marketer, from 1985 to 1996. Mr.
Sivertson started his career at American Hospital Supply Corporation and held
various sales and marketing positions from 1976 to 1985, including as Vice
President of Marketing for the Convertors Division. Mr. Sivertson was elected as
a director of ATS Medical in January 2003. Mr. Sivertson also serves on the
board of directors of Dymedix Corporation.


Messrs. Buck and Koentopf have decided not to stand for reelection at our 2006
Annual Meeting of Shareholders.


AUDIT COMMITTEE; AUDIT COMMITTEE FINANCIAL EXPERT

Our Audit Committee is composed of the following non-employee directors: Messrs.
Buck, Koentopf and Munzenrider. Mr. Munzenrider currently serves as the Chairman
of the Audit Committee. All of the members of the Audit Committee are
independent for purposes of the Nasdaq listing requirements. Mr. Munzenrider
qualifies as an "audit committee financial expert" under the rules of the SEC.



                                       2
<PAGE>

SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

Section 16(a) of the Securities Exchange Act of 1934, as amended, requires our
directors and executive officers and all persons who beneficially own more than
10% of our outstanding shares of common stock to file with the SEC initial
reports of ownership and reports of changes in ownership of such common stock.
Directors, executive officers and 10% or more beneficial owners are also
required to furnish us with copies of all Section 16(a) reports they file. Based
solely on a review of the copies of such forms furnished to us, we believe that
our executive officers, directors and 10% shareholders complied with all Section
16(a) filing requirements applicable to them during 2005.

CODE OF CONDUCT

In 2004, we adopted a Code of Conduct for our employees, including our principal
executive officer, principal financial officer and principal accounting officer,
which is posted on our website (www.atsmedical.com). We intend to satisfy the
disclosure requirement under Item 5.05 of Form 8-K regarding an amendment to, or
waiver from a provision of the Code of Conduct by posting such information on
our website at the address specified above.

                                       3

<PAGE>

ITEM 11. EXECUTIVE COMPENSATION

SUMMARY COMPENSATION TABLE

The following table sets forth the cash and non-cash compensation for each of
the last three fiscal years awarded to or earned by our Chief Executive Officer
and the four other most highly compensated executive officers during 2005.

<TABLE>
<CAPTION>


                                                        ANNUAL                          LONG-TERM
                                                    COMPENSATION(1)                    COMPENSATION
                                                -----------------------      -------------------------------
                                                                              RESTRICTED        SECURITIES        ALL OTHER
                                                                              STOCK UNIT        UNDERLYING       COMPENSATION
NAME AND PRINCIPAL POSITION          YEAR       SALARY($)      BONUS($)      AWARDS($)(2)      OPTIONS(#)(3)       ($)(4)
---------------------------------    ----       ---------      --------      ------------      -------------     ------------
<S>                                  <C>        <C>            <C>            <C>              <C>               <C>
Michael D. Dale                      2005        350,000         77,788           638,000                 0                 0
   President and Chief Executive     2004        270,000        102,384                 0                 0                 0
   Officer                           2003        250,000        100,000                 0            50,000                 0

John R. Judd                         2005        169,600         24,143           159,500                 0             3,500
   Chief Financial Officer(5)        2004        160,000         36,972                 0                 0             3,205
                                     2003         27,792         22,869                 0           125,000                 0

Richard A. Curtis                    2005        203,958         54,916            95,700                 0             3,500
   Vice President, Marketing and     2004        193,325         42,611                 0                 0             3,250
   Business Development              2003        185,000         49,256                 0            20,000            13,000

Marc R. Sportsman                    2005        248,062         61,484            63,800                 0             4,055
   Vice President, Sales             2004        225,000         83,276                 0                 0             3,250
                                     2003        155,769        184,375                 0           270,000             3,000

Maria-Teresa Ajamil                  2005        197,144         51,296            73,200                 0             4,500
   Vice President, International     2004        170,961         85,272                 0           100,000             2,166
   Markets(6)                        2003              0              0                 0                 0                 0
</TABLE>
---------------------------

(1)  Perquisites totaling less than the smaller of $50,000 or 10% of the total
     salary and bonus for any of the executive officers have been omitted.

(2)  The restricted stock units granted in 2005 vest in four equal installments
     in January 2006, 2007, 2008 and 2009. The value of each executive officer's
     restricted stock units included in this column is determined by multiplying
     the closing market price of our common stock on the respective dates of
     grant of the awards by the number of units awarded. The named executive
     officers held restricted stock units as of December 31, 2005, with market
     values as of that date (calculated by multiplying the closing market price
     of our common stock on that date by the total number of restricted units
     held by each officer) as follows: Mr. Dale, 200,000 units valued at
     $552,000; Mr. Judd, 50,000 units valued at $138,000; Mr. Curtis, 30,000
     units valued at $82,800; Mr. Sportsman, 20,000 units valued at $55,200; and
     Ms. Ajamil 20,000 units valued at $55,200. Prior to vesting of the
     restricted stock units, the executive officers have no ownership or voting
     rights over the shares of our common stock underlying the restricted stock
     units. However, the executive officers are entitled to receive dividend
     equivalents on the restricted stock units awarded, whether vested or
     unvested, when and if dividends are declared by the Board of Directors on
     our common stock.

(3)  Represents stock options granted with an exercise price per share at least
     equal to the fair market value of our common stock on the date of grant.

(4)  All 2005 amounts consist of matching contributions to the ATS Medical
     401(k) Plan, which is generally available to all employees.

(5)  Mr. Judd has served as our Chief Financial Officer since October 2003.

(6)  Ms. Ajamil has served as our Vice President, International Markets since
     January 2004.

                                       4


<PAGE>

OPTION GRANTS IN LAST FISCAL YEAR

We made no option grants to the executive officers listed in the Summary
Compensation Table above during 2005.

AGGREGATED OPTION EXERCISES IN LAST FISCAL YEAR AND FISCAL YEAR-END OPTION
VALUES

None of the executive officers named in the Summary Compensation Table exercised
stock options during 2005. The following table contains information regarding
the unexercised options held by such executive officers as of December 31, 2005.

<TABLE>
<CAPTION>
                                                         NUMBER OF SECURITIES           VALUE OF UNEXERCISED
                                                        UNDERLYING UNEXERCISED              IN-THE-MONEY
                                                          OPTIONS AT FISCAL              OPTIONS AT FISCAL
                         SHARES                               YEAR-END(#)                  YEAR-END($)(1)
                        ACQUIRED                    ------------------------------  ----------------------------
                           ON           VALUE
NAME                   Exercise(#)    Realized($)   EXERCISABLE    UNEXERCISABLE    EXERCISABLE    UNEXERCISABLE
-------------------    -----------    -----------   -----------   ---------------   -----------    -------------
<S>                    <C>             <C>          <C>           <C>               <C>             <C>
Michael D. Dale                  0              0       250,000          300,0000       478,000          791,000

John R. Judd                     0              0       125,000            50,000             0          138,000

Richard A. Curtis                0              0       113,750            61,250       209,906          152,769

Marc R. Sportsman                0              0       145,000           145,000       217,500          272,700

Maria-Teresa Ajamil              0              0       100,000            20,000             0           55,200
</TABLE>

------------------
(1)  Value represents the difference between the last sale price of our common
     stock on December 31, 2005, and the exercise price of the options.

COMPENSATION AGREEMENTS

Michael D. Dale has served as our President and Chief Executive Officer since
October 2002 pursuant to an employment agreement dated September 18, 2002. Mr.
Dale's initial annual base salary under the agreement was $250,000, which was
increased to $270,000 in 2004. In 2005, the board of directors increased Mr.
Dale's salary to $350,000. The board of directors granted a bonus of $77,788 to
Mr. Dale, which was paid to him in February 2006, as reward for achievement of
certain individual goals and company performance objectives based on net sales
and operating income (loss) established by the board of directors. The
employment agreement may be terminated at will by either party, provided that if
we terminate the agreement without cause, Mr. Dale would be entitled to a
severance payment equal to twelve months salary. The agreement also contains a
non-competition obligation pursuant to which Mr. Dale agrees not to compete with
us during the term of the agreement and for a period of one year following its
termination.

CHANGE IN CONTROL AGREEMENTS

We are entering into agreements with our officers providing for the payment of
certain benefits to the officers if their employment terminates following a
"change in control" of ATS Medical. The agreements provide for benefits if an
officer's employment is terminated within 24 months following a change in
control unless such termination was by us for cause, by the officer other than
for "good reason," or because of the officer's death. "Good reason" is defined
as the termination of employment as a result of either a diminution in the
officer's responsibilities, a reduction in salary or benefits, or a relocation
of our office of more than 35 miles. A "change in control" is generally defined
as an acquisition of more than 35% of our outstanding common stock by any person
or group, the merger or sale of ATS Medical or the replacement of a majority of
our board of directors with directors not recommended by the existing board of
directors. The agreements provide for lump sum payments following

                                       5

<PAGE>

termination in amounts equal to two times the officer's base salary, as limited
by Section 280G of the Internal Revenue Code of 1986, as amended. In addition,
we will provide such officer with health and dental benefits for up to 24 months
following termination. If there had been a change in control of ATS Medical as
of the end of 2005 and the employment of the executive officers named in the
Summary Compensation Table had been immediately terminated, Messrs. Dale, Judd,
Curtis and Sportsman and Ms. Ajamil would have been entitled to receive,
pursuant to the terms of the agreements, lump sum payments upon termination of
$700,000, $339,200, $407,916, $496,124 and $430,000, respectively.

COMPENSATION OF DIRECTORS

We pay each of our directors $15,000 as an annual retainer, payable quarterly,
for service on our board of directors. An additional $5,000 annual retainer,
payable quarterly, is paid to the chairs of the Audit Committee and the
Personnel and Compensation Committee. In addition, directors are paid $1,000 for
each board meeting attended in person and $500 for each board meeting attended
telephonically. Audit committee members are paid an additional $500 for each
meeting of the Audit Committee attended. We also reimburse our directors for
travel-related expenses.

Upon their initial election to the board of directors, each outside director
receives an option to purchase 5,000 shares of our common stock at the fair
market value on the date of election under the 2000 Stock Incentive Plan. Upon
each reelection, each outside director receives an option to purchase 2,500
shares of our common stock at the fair market value on the date of reelection
under the plan.

                                       6

<PAGE>

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND
         RELATED STOCKHOLDER MATTERS

SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth security ownership information pertaining to
persons known by us to beneficially own more than 5% of our common stock, our
directors and director nominees, the executive officers named in the Summary
Compensation Table and all of our directors and executive officers as a group as
of February 1, 2006.

<Table>
<Caption>

                                                      COMMON STOCK BENEFICIALLY OWNED
                                               ----------------------------------------------
                                                AMOUNT AND NATURE OF         PERCENT OF CLASS
NAME OF BENEFICIAL OWNER                       BENEFICIAL OWNERSHIP(1)        OUTSTANDING(2)
--------------------------------------------   -----------------------       ----------------
<S>                                            <C>                           <C>
Austin W. Marxe and                                          1,877,404(3)                 6.0%
David M. Greenhouse
527 Madison Avenue, Suite 2600
New York, NY 10022

Deerfield Capital, L.P.                                      1,934,200(4)                 6.2%
780 Third Avenue, 37th Floor
New York, NY 10017

Maria-Teresa Ajamil........................                    138,254                      *
John D. Buck...............................                     21,250                      *
Richard A. Curtis..........................                    127,248                      *
Michael D. Dale............................                    397,902                    1.3%
John R. Judd...............................                    147,192                      *
David Koentopf.............................                      5,000                      *
Robert E. Munzenrider......................                     11,875                      *
Eric W. Sivertson..........................                     14,375                      *
Marc. R. Sportsman.........................                    220,577                      *

All directors and executive officers as a
group (9 persons)..........................                  1,083,673                    3.4%
</Table>

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

(1)  Includes the following shares that may be acquired within 60 days of
     February 1, 2006 through the exercise of stock options: Ms. Ajamil, 100,000
     shares; Mr. Buck, 11,250 shares; Mr. Curtis, 113,750 shares; Mr. Dale,
     250,000 shares; Mr. Judd, 125,000 shares; Mr. Koentopf, 5,000 shares; Mr.
     Munzenrider, 11,875 shares; Mr. Sivertson, 14,375 shares; Mr. Sportsman,
     207,500 shares; and all executive officers and directors as a group,
     838,750 shares.

(2)  The ownership percentage for each person or entity is calculated based on
     the number of shares outstanding as of February 1, 2006, and assuming that,
     with respect to each person, any options exercisable within 60 days by that
     person had been exercised and the underlying shares were outstanding.

(3)  The number of shares owned is based on a Schedule 13G filed by jointly by
     Justin W. Marxe and David M. Greenhouse on February 14, 2006, who are the
     controlling principals of AWM Investment Company, Inc. ("AWM"), the general
     partner of and investment adviser to Special Situations Cayman Fund, L.P.
     AWM also serves as the general partner of MGP Advisers Limited Partnership,
     the general partner of and investment adviser to Special Situations Fund
     III, L.P. and Special Situations Fund III QP, L.P. Mr. Marxe and Mr.
     Greenhouse are also members of MG Advisers L.L.C., the general partner of
     and investment adviser to Special Situations Private Equity Fund, L.P. The
     Schedule 13G indicates that Austin W. Marxe and David M. Greenhouse share
     sole voting and investment power over 347,890 shares of Common Stock owned
     by Special Situations Cayman Fund, L.P., 994,630 shares of Common Stock
     owned by Special Situations Fund III QP, L.P., 87,184 shares of Common
     Stock owned by Special Situations Fund III, L.P. and 447,700 shares of
     Common Stock owned by Special Situations Private Equity Fund, L.P.

                                       7

<PAGE>

(4)  The number of shares owned is based on a Schedule 13G filed jointly by
     Deerfield Capital, L.P., Deerfield Partners, L.P., Deerfield Management
     Company, Deerfield International Limited and Arnold H. Snider on February
     14, 2006. Deerfield Capital, L.P. is the investment advisor to Deerfield
     Partners, LP. Snider Capital is the general partner of Deerfield Capital
     L.P., and Arnold Snider is the President of Snider Capital. Deerfield
     Management Company is the investment advisor to Deerfield International
     Limited. Snider Management is the general partner of Deerfield Management
     Company and Arnold H. Snider is the President of Snider Management. The
     Schedule 13G indicates that Deerfield Capital, L.P. and Deerfield Partners,
     L.P. each have shared voting and dispositive power over 835,574 shares of
     common stock, Deerfield Management Company and Deerfield International
     Limited each have shared voting and dispositive power over 1,098,626 shares
     of common stock, and Arnold H. Snider has shared voting and dispositive
     power of 1,934,200 shares of common stock.

EQUITY COMPENSATION PLANS

The following table summarizes as of December 31, 2005 the shares of our common
stock subject to outstanding awards or available for future awards under our
equity compensation plans and arrangements.

<Table>
<Caption>

                                                                                     NUMBER OF SHARES REMAINING
                                                                                       AVAILABLE FOR FUTURE
                                 NUMBER OF SHARES                                      ISSUANCE UNDER EQUITY
                                   TO BE ISSUED             WEIGHTED-AVERAGE               COMPENSATION
                                 UPON EXERCISE OF           EXERCISE PRICE OF            PLANS (EXCLUDING
                               OUTSTANDING OPTIONS,       OUTSTANDING OPTIONS,           SHARES REFLECTED
       PLAN CATEGORY            WARRANTS AND RIGHTS        WARRANTS AND RIGHTS         IN THE FIRST COLUMN)
--------------------------     --------------------       --------------------       --------------------------
<S>                            <C>                        <C>                        <C>
Equity Compensation Plans
Approved by Shareholders                1,704,700                      $3.08                     1,986,911     (1)

Equity Compensation Plans
Not Approved by
Shareholders                            2,897,902                      $2.73                            --     (2)
                               --------------------       --------------------       --------------------------
Total                                   4,602,602                      $2.86                     1,986,911
                               ====================       ====================       ==========================
</Table>

--------------------
(1)  Includes shares remaining available under our 2000 Stock Incentive Plan
     (1,915,250 shares) and 1998 Employee Stock Purchase Plan (71,661 shares).

(2)  Nearly all of the 2,897,902 shares listed consist of individual stock
     options granted to new executives or employees as an inducement to their
     employment with us. These options have an exercise price equal to the fair
     market value of our common stock at the time of the grant, and vest ratably
     over two to four year periods. Most of the options have a life of 10 years
     and vesting accelerates upon a change of control of ATS Medical. We intend
     that these options shall not be Incentive Stock Options governed by the
     provisions of Section 422 of the Internal Revenue Code.

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

None.

                                       8

<PAGE>

ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES

Ernst & Young LLP, our independent registered public accounting firm, provides
both audit and non-audit services to us. The fee table below reports fees billed
or to be billed to us for professional services provided to us during 2005 and
2004. Based in part on its review of the nature and value of services provided
by Ernst & Young LLP, our Audit Committee has concluded that the provision of
non-audit services is compatible with maintaining Ernst & Young LLP's
independence. The Audit Committee has approved, pursuant to its pre-approval
policies described below, 100% of the services listed below.

<Table>
<Caption>
                              2005                 2004
                       ------------------   ------------------
<S>                    <C>                  <C>
Audit Fees (1)         $          320,000   $          276,740

Audit-Related Fees     $                0   $                0

Tax Fees (2)           $                0   $           53,750

All Other Fees         $                0   $                0
                       ------------------   ------------------

Total Fees             $          320,000   $          330,490
                       ==================   ==================
</Table>

--------------------
(1)  The increase in audit fees from 2004 to 2005 was due primarily to audit
     work relating to our internal control over financial reporting, as required
     by the Sarbanes-Oxley Act of 2002.

(2)  Tax fees for 2004 were for tax consulting and compliance services.



All services provided by our independent registered public accounting firm,
Ernst & Young LLP, are subject to pre-approval by our Audit Committee. The Audit
Committee has authorized the Chair of the Audit Committee to approve services by
Ernst & Young LLP in the event there is a need for such approval prior to the
next Audit Committee meeting. However, a full report of any such interim
approvals must be given at the next Audit Committee meeting. Before granting any
approval, the Audit Committee (or the Committee Chair, if applicable) must
receive: (1) a detailed description of the proposed service; (2) a statement
from management as to why they believe Ernst & Young LLP is best qualified to
perform the service; and (3) an estimate of the fees to be incurred. Before
granting any approval, the Audit Committee (or the committee Chair, if
applicable) gives due consideration to whether approval of the proposed service
will have a detrimental impact on Ernst & Young LLP's independence.


                                     PART IV

ITEM 15 EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

Note: Item 15 in the Original Filing is unchanged except for the filing of
additional certifications pursuant to Section 302 of the Sarbanes-Oxley Act of
2002.

EXHIBIT
NUMBER                               DESCRIPTION
-------  -----------------------------------------------------------------------

31.1     Certification of Chief Executive Officer pursuant to Rule 13a-14(a) and
         Rule 15d-14(a) of the Securities Exchange Act, as amended.

31.2     Certification of Chief Financial Officer pursuant to Rule 13a-14(a) and
         Rule 15d-14(a) of the Securities Exchange Act, as amended.

                                       9


<PAGE>


                                   SIGNATURE



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



Dated: April 27, 2006                    ATS MEDICAL, INC.



                                        By /s/ Michael D. Dale
                                           -------------------------------------
                                           Michael D. Dale
                                           Chief Executive Officer


                                      10

<PAGE>

                                  EXHIBIT INDEX

EXHIBIT
NUMBER                               DESCRIPTION
-------  -----------------------------------------------------------------------
31.1     Certification of Chief Executive Officer pursuant to Rule 13a-14(a) and
         Rule 15d-14(a) of the Securities Exchange Act, as amended.

31.2     Certification of Chief Financial Officer pursuant to Rule 13a-14(a) and
         Rule 15d-14(a) of the Securities Exchange Act, as amended.

                                       11