<PAGE>
                                                                     Exhibit 4.1

                   FORM OF 6% CONVERTIBLE SENIOR NOTE DUE 2025

                                   ----------

                                ATS MEDICAL, INC.

                             [FORM OF FACE OF NOTE]

[THE FOLLOWING PARAGRAPH SHALL APPEAR ON THE FACE OF EACH RESTRICTED NOTE.]

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED (THE "SECURITIES ACT") OR APPLICABLE
STATE SECURITIES LAWS. THIS SECURITY MAY NOT BE OFFERED FOR SALE, SOLD,
TRANSFERRED OR ASSIGNED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT
FOR THE SECURITIES UNDER THE SECURITIES ACT AND APPLICABLE STATE SECURITIES LAWS
OR AN EXEMPTION THEREFROM.

[THE FOLLOWING PARAGRAPH SHALL APPEAR ON THE FACE OF EACH GLOBAL NOTE.]

Unless this Note is presented by an authorized representative of The Depository
Trust Company, a New York corporation ("DTC"), to the Issuer or its agent for
registration of transfer, exchange or payment, and any Note issued is registered
in the name of Cede & Co. or in such other name as is requested by an authorized
representative of DTC (and any payment is made to Cede & Co. or to such other
entity as is requested by an authorized representative of DTC), ANY TRANSFER,
PLEDGE OR OTHER USE HEREOF FOR VALUE OR OTHERWISE BY OR TO ANY PERSON IS
WRONGFUL inasmuch as the registered owner hereof, Cede & Co., has an interest
herein.

                                ATS MEDICAL, INC.
                       6% Convertible Senior Note due 2025

No. _____                                                       $_______________

CUSIP No. _____________

     ATS Medical, Inc., a corporation duly organized and validly existing under
the laws of the State of Minnesota (herein called the "Company", which term
includes any successor corporation under the Indenture referred to on the
reverse hereof), for value received hereby promises to pay to
____________________, or registered assigns, the principal sum of ___________
United States Dollars on October 15, 2025 and to pay interest on said principal
sum semi-annually on April 15 and October 15 of each year (each, an "Interest
Payment Date"),

<PAGE>

commencing April 15, 2006, at the rate per annum specified in the title of this
Note, accrued from the most recent date to which interest has been paid or, if
no interest has been paid, from October 7, 2005. The interest so payable on any
April 15 or October 15 will be paid to the person in whose name this Note (or
one or more Predecessor Notes) is registered at the close of business on the
record date, which shall be the 4th day of the month in which the Interest
Payment Date shall occur, whether or not such date is a Business Day; provided
that any such interest not punctually paid or duly provided for shall be payable
as provided in the Indenture. Each payment of interest on this Note shall
include interest to, but excluding, the date of such payment. Payment of the
principal of and interest accrued on this Note (including Liquidated Damages, if
any) shall be made at the office or agency of the Company maintained for that
purpose, which shall initially be the office or agency of the Trustee in
Minneapolis, Minnesota, specified in the Indenture, or at any other office or
agency permitted by the Indenture, in such lawful money of the United States of
America as at the time of payment shall be legal tender for the payment of
public and private debts; provided, that interest may, at the option of the
Company, be paid by check mailed to the address of the holder hereof on the Note
Register; provided further, however, that, with respect to any holder of Notes
with an aggregate principal amount equal to or in excess of Five Hundred
Thousand United States Dollars ($500,000), interest on such holder's Notes shall
be paid by wire transfer in immediately available funds to any bank located in
the United States in accordance with the written wire transfer instruction
supplied by such holder from time to time to the Trustee and paying agent (if
different from the Trustee) in writing at least five (5) Business Days prior to
the applicable record date.

     Reference is made to the further provisions of this Note set forth on the
reverse hereof, including, without limitation, provisions giving a holder of
this Note the right to convert this Note into Common Stock of the Company on the
terms and subject to the limitations referred to on the reverse hereof and as
more fully specified in the Indenture. Such further provisions shall for all
purposes have the same effect as though fully set forth at this place.

     This Note shall be deemed to be a contract made under the laws of the State
of New York and for all purposes shall be construed in accordance with the
internal laws of the State of New York without giving effect to any choice of
law or conflict of law provision or rule (whether of the State of New York or
any other jurisdictions) that would cause the application of the laws of any
jurisdictions other than the State of New York.

     This Note shall not be valid or become obligatory for any purpose until the
certificate of authentication hereon shall have been manually signed by the
Trustee or a duly authorized authenticating agent under the Indenture.


                                        2

<PAGE>

     IN WITNESS WHEREOF, the Company has caused this Note to be duly executed.

                                        ATS MEDICAL, INC.

                                        ________________________________________
                                        [Name, Title]

Attest:

____________________________________
[Name, Title]

TRUSTEE'S CERTIFICATE OF AUTHENTICATION

WELLS FARGO BANK, NATIONAL ASSOCIATION,
as Trustee, certifies that this is one
of the Notes described in the
within-named Indenture.

Dated:
       --------------


By:
    ---------------------------------
    Authorized Signatory


                                        3

<PAGE>

                            [FORM OF REVERSE OF NOTE]
                                ATS MEDICAL, INC.
                       6% Convertible Senior Note due 2025

     This Note is one of a duly authorized issue of Notes of the Company,
designated as its 6% Convertible Senior Notes due 2025 (herein called the
"Notes"), limited (except as otherwise provided in the Indenture) to the
aggregate principal amount outstanding of _______________ United States Dollars,
($____________) all issued or to be issued under and pursuant to an Indenture
dated as of October 7, 2005 (herein called the "Indenture"), between the Company
and Wells Fargo Bank, National Association (herein called the "Trustee"), to
which Indenture and all indentures supplemental thereto reference is hereby made
for a full description of the rights, limitations of rights, obligations, duties
and immunities thereunder of the Trustee, the Company and the holders of the
Notes. All capitalized terms used herein without definition shall have the
meaning set forth in the Indenture.

     In case an Event of Default, as defined in the Indenture, shall have
occurred and be continuing, the principal of and premium, if any, on all Notes
and the interest accrued thereon (including Liquidated Damages to the extent
accrued and unpaid) may be declared, and upon said declaration shall become, due
and payable, in the manner, with the effect and subject to the conditions
provided in the Indenture. Liquidated damages paid pursuant to Section 15.2 of
the Indenture, if any, shall be paid within ten (10) Business Days after the end
of each month with respect to which such liquidated damages have accrued
pursuant to Section 15.2 in the same manner as interest is paid. Liquidated
Damages on the Notes paid pursuant to Section 2(f) of the Registration Rights
Agreement, if any, shall be paid at the times and in the manner provided
therein.

     The Indenture contains provisions permitting the Company and the Trustee in
certain limited circumstances, without the consent of the holders of the Notes,
and in other circumstances, with the consent of the holders of not less than a
majority in aggregate principal amount of the Notes at the time outstanding,
evidenced as in the Indenture provided, to execute amendments to the Indenture
or supplemental indentures adding any provisions to or changing in any manner or
eliminating any of the provisions of the Indenture or of any supplemental
indenture or modifying in any manner the rights of the holders of the Notes;
provided, however, that no such amendment or supplemental indenture shall (i)
extend the fixed maturity of any Note, or reduce the rate or extend the time of
payment of interest thereon, or reduce the principal amount thereof or premium,
if any, thereon, or reduce any amount payable on redemption or repurchase
thereof, impair or change in any respect adverse to the holder of Notes the
obligation of the Company to repurchase any Note at the option of the holder in
accordance with Article XVI of the Indenture, or impair or adversely affect the
right of any Noteholder to institute suit for the payment thereof, or change the
currency in which the Notes are payable, or impair or change in any respect
adverse to the Noteholders the right to convert the Notes into Common Stock
subject to the terms set forth in the Indenture, including Section 15.6, or to
subordinate the Notes in right of payment to other indebtedness, in each such
case without the consent of the holder of each Note so affected, or (ii) reduce
the aforesaid percentage of Notes, the holders of which are required to consent
to any such supplemental indenture, without the consent of the holders of all
Notes then outstanding. In addition, any amendment or supplemental indenture


                                        4

<PAGE>

that disproportionately affects the rights of a Noteholder or a class of
Noteholder shall require the prior consent of such Noteholder or the prior
consent of Noteholders holding a majority of the principal amount of Notes then
held by such class, as applicable.

     It is also provided in the Indenture that the holders of not less than a
majority in aggregate principal amount of the Notes at the time outstanding may
on behalf of the holders of all of the Notes waive any past or existing default
or Event of Default under the Indenture and its consequences except (i) a
default in the payment of interest or premium, if any, on, or the principal of,
the Notes when due, (ii) a failure by the Company to convert any Notes into
Common Stock or (iii) a default in respect of a covenant or provisions of the
Indenture which under Article XI thereof cannot be modified or amended without
the consent of all affected holders of Notes then outstanding.

     Interest on the Notes shall be computed on the basis of a 360-day year
comprised of twelve 30-day months.

     The Notes are issuable in registered form without coupons in denominations
of One Thousand United States Dollars ($1,000) principal amount and integral
multiples thereof. At the office of the Trustee or the Company referred to on
the face hereof, and in the manner and subject to the limitations provided in
the Indenture, without payment of any service charge but with payment of a sum
sufficient to cover any tax, assessments or other governmental charges that may
be imposed in connection with any exchange or registration of transfer of Notes,
Notes may be exchanged for a like aggregate principal amount of Notes of other
authorized denominations. All transfers are subject to the restrictions thereon
provided in the Indenture.

     From and after October 20, 2008, the Company may, at its option, redeem all
or any part of the Notes, upon notice as set forth in the Indenture, and the
Company shall pay each holder of Notes redeemed a redemption price equal to the
principal amount of such Notes, plus accrued and unpaid interest thereon, if
any, to, but excluding, the date of redemption, subject to the proviso in the
final sentence of this paragraph. If notice of redemption has been given as
provided in the Indenture, the Notes or portion of Notes called for redemption
shall, unless converted into Common Stock pursuant to the terms of the
Indenture, become due and payable on the date and at the place or places stated
in such notice at the applicable redemption price and interest accrued to, but
excluding, the date fixed for redemption, and on and after such date (unless the
Company shall default in the deposit of the amount of money sufficient to redeem
such Notes) interest on the Notes or portion of Notes so called for redemption
shall cease to accrue and such Notes shall cease after the close of business on
the last Business Day prior to the date fixed for redemption to be convertible
into Common Stock and, except as provided in Sections 8.5 and 13.4 of the
Indenture, to be entitled to any benefit or security under the Indenture, and
the holders of such Notes shall have no right in respect of such Notes except
the right to receive the redemption price and unpaid interest to, but excluding,
the date fixed for redemption. On presentation and surrender of such Notes at a
place of payment specified in such notice, such Notes or the specified portions
thereof to be redeemed shall be paid and redeemed by the Company at the
applicable redemption price and interest accrued thereon to, but excluding, the
date fixed for redemption; provided that, if the applicable redemption date
falls after the record date for an Interest Payment Date and before the relevant
Interest Payment Date, then the semi-annual payment of interest becoming due on
such Interest Payment Date shall be


                                        5

<PAGE>

paid to the holders of such Notes registered as such on the relevant record date
in the manner provided for the payment of interest generally and shall not be
paid to the holders surrendering the Notes when they do so.

     The Notes are not subject to redemption through the operation of any
sinking fund.

     Upon the occurrence of a "Repurchase Event," the Noteholder has the right,
at such holder's option, to require the Company to repurchase all of such
holder's Notes, or any portion thereof (in the principal amounts of One Thousand
United States Dollars ($1,000) or integral multiples thereof) on the date set by
the Company that is no earlier than the Business Day immediately following the
earliest date permitted under Rule 13e-4 or Rule 14e-1 under the Exchange Act
(or any successor rules), if either such rule is applicable, and no later than
sixty (60) calendar days after the date of the notice of such Repurchase Event
that the Company is required by the Indenture to send (or, if such 60th day is
not a Business Day, the next succeeding Business Day) at a price equal to 100%
of the principal amount of the Notes such holder elects to require the Company
to repurchase together, in each case, with accrued interest, if any, to, but
excluding, the date fixed for repurchase (the "Repurchase Price"); provided that
if such Repurchase Date occurs after a record date or special record date and
before the related Interest Payment Date or special interest payment date, the
amount payable on such Interest Payment Date or special interest payment date,
shall be paid to the recordholder at the close of business on the record date or
special record date as provided in Section 2.3 of the Indenture and shall not
constitute part of the Repurchase Price. In addition, Notes shall be purchased
by the Company at the option of the holder on October 15, 2010, October 15, 2015
and October 15, 2020 (each, also a "Repurchase Date"), at the Repurchase Price.
If a redemption date pursuant to Article III of the Indenture shall occur prior
to any Repurchase Date established pursuant to a Company Notice under Section
16.2 of the Indenture, provided that the Company shall have deposited or set
aside an amount of money sufficient to redeem such Notes as set forth in Section
3.2 of the Indenture on or before such Repurchase Date, all such Notes shall be
redeemed pursuant to Article III of the Indenture and the repurchase rights
under Article XVI of the Indenture shall have no effect.

     Subject to the provisions of the Indenture, the holder hereof has the
right, at its option, at any time following the date of original issuance of the
Notes and prior to the close of business on October 15, 2025 (except that, with
respect to any Note or portion of a Note that shall be called for redemption or
shall have been noticed for automatic conversion, such right shall terminate,
except as otherwise provided in the Indenture, at the close of business on the
last Business Day prior to the date fixed for redemption or automatic conversion
unless the Company shall default in payment due upon redemption or the delivery
of shares on automatic conversion thereof), to convert the principal hereof or
any portion of such principal which is One Thousand United States Dollars
($1,000) or an integral multiple thereof, into that number of fully paid and
non-assessable shares of the Company's Common Stock (as such shares shall then
be constituted), obtained by dividing the principal amount of this Note or
portion thereof surrendered for conversion by the Conversion Price of $4.20, or
such Conversion Price as adjusted from time to time as provided in the
Indenture. In order to exercise the conversion privilege, the holder must take
the actions specified in the Indenture. These actions include (i) delivery of a
conversion notice, (ii) if this Note or portion hereof is surrendered for
conversion during the period from the close of business on the record date for
any Interest Payment Date through the close of business on the last Business Day
prior to such Interest Payment Date, pay by wire transfer of


                                        6

<PAGE>

immediately available funds or other method acceptable to the Company, an amount
equal to the interest otherwise payable on such Interest Payment Date on the
principal amount being converted; provided, however, that no such payment need
be made if there shall exist at the time of conversion a default in the payment
of interest on the Notes (subject to certain exceptions specified in the
Indenture), (iii) pay by wire transfer of immediately available funds or other
method acceptable to the Company the transfer taxes, if any, required pursuant
to the Indenture and (iv) surrender the Note to be converted in whole or in
part. No fractional shares of Common Stock or scrip representing fractional
shares shall be issued upon conversion, but a cash adjustment in lieu of such
fractional share will be paid to the holder, as provided in the Indenture.

     If a the holder of this Note elects to convert all or any portion of this
Note into shares of Common Stock and the Company does not have a sufficient
number of authorized shares of Common Stock to deliver upon conversion, the
Company may choose to satisfy all or any portion of its conversion obligation in
cash in the manner prescribed in the Indenture. For purposes of the foregoing
sentence, the Company, when determining whether it has a sufficient number of
authorized shares of Common Stock to deliver upon conversion, may treat as
outstanding any shares reserved (as of the date of this Indenture) by the
Company's Board of Directors for a specific purpose including issuance under any
existing stock option or other equity plan of the Company or other obligation of
the Company to issue shares of Common Stock.

     The Company may, at its option, automatically convert all or a portion of
the Notes (an "Automatic Conversion") at any time prior to October 15, 2025 if
the Closing Price (as defined in the Indenture) per share of the Common Stock
has exceeded one hundred and fifty percent (150%) of the Conversion Price then
in effect for at least fifteen (20) Trading Days within a period of thirty (30)
consecutive Trading Days ending within five (5) Trading Days of the date the
Company gives to all holders of Notes a notice of the Automatic Conversion,
provided that either (x) a registration statement covering the resale of the
Conversion Shares is effective and available for use from the date of the notice
of Automatic Conversion through and including the earlier of the date on which
the Automatic Conversion becomes effective or the last date on which the
registration statement is required to be kept effective under the terms of the
Registration Rights Agreement, or (y) the shares of Common Stock issuable upon
the Automatic Conversion may be sold pursuant to Rule 144(k) under the
Securities Act (assuming, for purposes of such determination, that no recipient
of Conversion Shares is an "affiliate" of the Company within the meaning of such
Rule and that all recipients of Conversion Shares have held the Notes since the
date of their original issuance). The Company may only elect an Automatic
Conversion with respect to all or any part of the Notes if it has, as of the
date of the Automatic Conversion Notice, sufficient shares of Common Stock
authorized and available for issuance on conversion of the Notes so called for
Automatic Conversion. If the effective date of an Automatic Conversion is prior
to October 15, 2008, the Company shall make an additional payment in cash or, at
the election of the Company under certain circumstances, in shares of Common
Stock, to each holder of Notes (or portion thereof) with respect to the Notes
(or portion thereof) converted, in an amount equal to $181.33 per each One
Thousand United States Dollars ($1,000) principal amount of the holder's Notes
(or portion thereof) (the "Company Conversion Provisional Payment"), less the
amount of any interest actually paid on the holder's Notes (or portion thereof)
prior to the effective date of the Automatic Conversion (and, if the relevant


                                        7

<PAGE>

Notes are converted after a record date and before the related Interest Payment
Date, less interest payable on such Notes (or portion thereof) on such Interest
Payment Date). Except as provided in the immediately preceding sentence, if the
Automatic Conversion Date with respect to any Notes (or portions thereof)
subject to an Automatic Conversion occurs following a record date and prior to
the related Interest Payment Date, then unless the Company defaults in its
obligation to deliver the shares of Common Stock issuable on such Automatic
Conversion. the Company shall not be obligated to pay any interest on such
Interest Payment Date, either to the holder of such Notes (or portions thereof)
at the close of business on the relevant record date or to the holder of such
Notes (or portions thereof) to whom the Company issues the shares of Common
Stock issuable on the Automatic Conversion. Common Stock used to pay any Company
Conversion Provisional Payment shall be valued at ninety-five percent (95%) of
the Closing Prices per share of the Common Stock for the ten (10) consecutive
Trading Days ending on and including the second Trading Day immediately
preceding the Conversion Date.

     If the Company elects to convert all or a portion of the Notes pursuant to
its Automatic Conversion right, the Company, or at its request (which must be
received by the Trustee at least five (5) Business Days prior to the date the
Trustee is requested to give notice as described below unless a shorter period
is agreed to by the Trustee), the Trustee in the name of and at the expense of
the Company, shall send or cause to be sent a notice of the Automatic Conversion
not more than thirty (30) days but not less than five (5) days before the date
of effectiveness of the Automatic Conversion as set forth in the Indenture.

     In connection with any redemption of Notes, the Company may arrange for the
purchase and conversion of any Notes not converted prior to the expiration of
such conversion right by an agreement with one or more investment bankers or
other purchasers to purchase such Notes by paying to the Trustee in trust for
the Noteholders, on or before the date fixed for redemption, an amount not less
than the applicable redemption price and interest accrued to the date fixed for
redemption of such Notes.

     [INCLUDE EITHER OF THE FOLLOWING PARAGRAPHS ONLY BASED UPON HOLDER'S
ELECTION UNDER SECTION 2(K) OF THE SECURITIES PURCHASE AGREEMENT] [Conversion
Limitation. The holder hereby agrees that in no event will it convert any of the
Notes in excess of the number of such Notes upon the conversion of which (x) the
number of shares of Common Stock beneficially owned by such holder (other than
the shares which would otherwise be deemed beneficially owned except for being
subject to a limitation on conversion analogous to the limitation contained in
this paragraph) plus (y) the number of shares of Common Stock issuable upon the
conversion of such Notes would be equal to or exceed 9.99% of the number of
shares of Common Stock then issued and outstanding (after giving effect to such
conversion), it being the intent of the Company and the holder that the holder
not be deemed at any time to have the power to vote or dispose of greater than
9.99% of the number of shares of Common Stock issued and outstanding. As used
herein, beneficial ownership shall be determined in accordance with Section
13(d) of the Securities Exchange Act of 1934, as amended (the "Exchange Act").
To the extent that the limitation contained in this paragraph applies (and
without limiting any rights the Company may otherwise have), the Company may
rely on the holder's determination of whether the Notes are convertible pursuant
to the terms hereof, the Company having no obligation whatsoever to verify or
confirm the accuracy of such determination, and the submission of the Conversion
Notice by the holder shall


                                        8

<PAGE>

be deemed to be the holder's representation that the Notes specified therein are
convertible pursuant to the terms hereof. Nothing contained herein shall be
deemed to restrict the right of a holder to convert the Notes at such time as
the conversion thereof will not violate the provisions of this paragraph.]

     [Each holder hereby agrees that in no event will it convert any of the
Notes in excess of the number of such Notes upon the conversion of which (x) the
number of shares of Common Stock beneficially owned by such holder (other than
the shares which would otherwise be deemed beneficially owned except for being
subject to a limitation on conversion analogous to the limitation contained in
this paragraph) plus (y) the number of shares of Common Stock issuable upon the
conversion of such Notes, would be equal to or exceed 4.99% of the number of
shares of Common Stock then issued and outstanding (after giving effect to such
conversion), it being the intent of the Company and the holder that the holder
not be deemed at any time to have the power to vote or dispose of greater than
4.99% of the number of shares of Common Stock issued and outstanding. As used
herein, beneficial ownership shall be determined in accordance with Section
13(d) of the Securities Exchange Act of 1934, as amended (the "Exchange Act").
To the extent that the limitation contained in this paragraph applies (and
without limiting any rights the Company may otherwise have), the Company may
rely on the holder's determination of whether the Notes are convertible pursuant
to the terms hereof, the Company having no obligation whatsoever to verify or
confirm the accuracy of such determination, and the submission of the Conversion
Notice by the holder shall be deemed to be the holder's representation that the
Notes specified therein are convertible pursuant to the terms hereof. Nothing
contained herein shall be deemed to restrict the right of a holder to convert
the Notes at such time as the conversion thereof will not violate the provisions
of this paragraph.]

     Prior to due presentment for the registration of a transfer of this Note,
the Trustee, any agent and the Company may deem and treat the Person in whose
name this Note is registered as the absolute owner of this Note, for the purpose
of receiving payment of principal of and interest on this Note and for all other
purposes and none of the Trustee, any agent or the Company shall be affected by
any notice to the contrary. All such payments so made to, or upon the order of,
such registered holder shall be valid, and, to the extent of the sum or sums so
paid, effectual to satisfy and discharge the liability for monies payable on
this Note.

     No direct or indirect partner, employee, incorporator, shareholder,
director or officer, as such, past, present or future of the Company or any
successor Person or any Subsidiary or any of the Company's Affiliates, shall
have any personal liability in respect of the obligations of the Company under
this Note or the Indenture by reason of his, her or its status as such partner,
employee, incorporator, shareholder, director or officer. The holder hereof by
accepting this Note waives and releases all such liability. Such waiver and
release are part of the consideration for the issuance of this Note.


                                        9

<PAGE>

                                  ABBREVIATIONS

     The following abbreviations, when used in the inscription of the face of
this Note, shall be construed as though they were written out in full according
to applicable laws or regulations:

     TEN COM - as tenants in common           UNIF GIFT MIN ACT -

Custodian                                     __________________________________
                                                            (Cust)

     TEN ENT - as tenants by the entireties   __________________________________
                                                           (Minor)

     JT TEN - as joint tenants with right
     of survivorship and not as tenants       Uniform Gifts to Minors Act
     in common                                __________________________________
                                                           (State)

     Additional abbreviations may also be used though not in the above list.


                                       10

<PAGE>

              SCHEDULE OF EXCHANGES OF INTERESTS IN THE GLOBAL NOTE

The following exchanges of a part of this Global Note for an interest in another
Global Note, or exchanges of a part of another Global Note for an interest in
this Global Note, have been made:

<TABLE>
<CAPTION>
                       Amount of          Amount of       Principal Amount
                      decrease in        increase in      of this Global        Signature of
                   Principal Amount   Principal Amount    Note following     authorized officer
                    of this Global     of this Global    such decrease (or      of Trustee or
Date of Exchange         Note               Note             increase)         Note Custodian
----------------   ----------------   ----------------   -----------------   ------------------
<S>                <C>                <C>                <C>                 <C>

</TABLE>


                                       11