Document:

EX-10.4

EXHIBIT 10.4

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED (THE “SECURITIES ACT”), OR ANY STATE SECURITIES LAWS. THIS WARRANT AND THE
UNDERLYING SECURITIES MAY NOT BE TRANSFERRED UNLESS (I) THIS WARRANT AND THE UNDERLYING SECURITIES
HAVE BEEN REGISTERED FOR SALE PURSUANT TO THE SECURITIES ACT, (II) THIS WARRANT AND THE UNDERLYING
SECURITIES MAY BE SOLD PURSUANT TO RULE 144(K) OR (III) THE COMPANY HAS RECEIVED AN OPINION OF
COUNSEL REASONABLY SATISFACTORY TO IT THAT SUCH TRANSFER MAY LAWFULLY BE MADE WITHOUT REGISTRATION
UNDER THE SECURITIES ACT OR QUALIFICATION UNDER APPLICABLE STATE SECURITIES LAWS.

WARRANT

THIS CERTIFIES THAT, for value received, ALTA PARTNERS VIII, L.P. (the “Holder”) is
entitled to subscribe for and purchase a warrant (i) to purchase, after Shareholder Approval (as
defined in Section 2(a) below) is obtained, 1,960,000 fully paid and nonassessable shares (the
“Shares”) of common stock, par value $0.01 per share (the “Common Stock”), of ATS
Medical, Inc., a Minnesota corporation (the “Company”), or (ii) to receive, prior to
Shareholder Approval (as defined in Section 2(a) below) being obtained, the equivalent cash value
thereof, in the manner described in Section 2(a) below, at a price per share equal to $1.65 (such
price and such other price as shall result, from time to time, from the adjustments specified in
Section 4 hereof is herein referred to as the “Warrant Price”), upon the terms and subject
to the conditions hereinafter set forth. This warrant is being issued on this 28th day of June,
2007 (the “Date of Grant”).

1. Term. The right represented by this warrant is exercisable, in whole or in part, at any
time and from time to time from the earlier of June      , 2008 or the date on which Shareholder
Approval is obtained (the “Initial Exercise Date”) until the seven (7) year anniversary of the Date
of Grant.

2. Method of Exercise; Payment; Issuance of New Warrant. Subject to Section 1 hereof, the
purchase right represented by this warrant may be exercised by the Holder hereof, in whole or in
part and from time to time, at the election of the Holder hereof, after the Initial Exercise Date,
in the manner described below:

	(a)	 	if the Company has not received the requisite approval of its shareholders to issue shares of
Common Stock to the Holder upon exercise of this warrant (“Shareholder Approval”),
then the Holder shall be entitled (i) to exercise this warrant, in whole or in part, at any
time and from time to time from June 28, 2008, by  surrendering this warrant (with the notice
of exercise substantially in the form attached hereto as Exhibit A-1 duly completed and
executed) at the principal office of the Company, and (ii) to receive, upon such exercise of
this warrant, cash from the Company in an amount equal to the difference between (A) the
then-current “fair market value” (as defined under Section 9(c) below) of the Shares, and
(B) the Warrant Price, multiplied by the number of Shares to which such exercise relates; or

	(b)	 	if the Company has received Shareholder Approval at the time Holder elects to exercise this
warrant, then the Holder shall (i) surrender this warrant (with the notice of exercise
substantially in the form attached hereto as Exhibit A-1 duly completed and executed) at the
principal office of the Company and by the payment to the Company, by certified or bank check,
or by wire transfer to an account designated by the Company (a “Wire Transfer”) of an
amount equal to the then applicable Warrant Price multiplied by the number of Shares then
being purchased; or (ii) exercise the “net issuance” right provided for in Section 9 hereof.
In the event of any exercise of the rights represented by this warrant pursuant to this
Section 2(b), certificates for the shares of stock so purchased shall be delivered to the
Holder hereof as soon as practicable and in any event within three (3) business days after
such exercise and, unless this warrant has been fully exercised or expired, a new warrant
representing the portion of the Shares, if any, with respect to which this warrant shall not
then have been exercised shall also be issued to the Holder hereof as soon as practicable and
in any event within such thirty-day period; provided, however, if requested by the Holder of
this warrant, the Company shall use reasonable efforts to cause its transfer agent to deliver
the certificate representing Shares issued upon exercise of this warrant to a broker or other
person (as directed by the Holder exercising this warrant) within the time period required to
settle any trade made by the Holder after exercise of this warrant.

The person or persons in whose name(s) any certificate(s) representing shares of Common Stock shall
be issuable upon exercise of this warrant shall be deemed to have become the holder(s) of record
of, and shall be treated for all purposes as the record holder(s) of, the shares represented
thereby (and such shares shall be deemed to have been issued) immediately prior to the close of
business on the date or dates upon which this warrant is exercised.

3. Stock Fully Paid; Reservation of Shares. All Shares that may be issued upon the
exercise of the rights represented by this warrant will, upon issuance pursuant to the terms and
conditions herein, be fully paid and nonassessable, and free from all preemptive rights and taxes,
liens and charges with respect to the issue thereof. During the period within which the rights
represented by this warrant may be exercised, the Company will at all times have authorized, and
reserved for the purpose of the issue upon exercise of the purchase rights evidenced by this
warrant, a sufficient number of shares of Common Stock to provide for the exercise of the rights
represented by this warrant. If at any time during the term of this warrant the number of
authorized but unissued shares of Common Stock shall not be sufficient to permit exercise of this
warrant, the Company will take such corporate action as may, in the opinion of its counsel, be
necessary to increase its authorized but unissued shares of Common Stock to such number of shares
as shall be sufficient for such purposes.

4. Adjustment of Warrant Price and Number of Shares. The number of shares of Common Stock
purchasable upon the exercise of this warrant and the Warrant Price shall be subject to adjustment
from time to time upon the occurrence of certain events, as follows:

	(a)	 	Reclassification or Merger. In case of any reclassification or change of securities
of the class issuable upon exercise of this warrant (other than a change in par value, or from
par value to no par value, or from no par value to par value, or as a result of a subdivision
or combination), or in case of any merger of the Company with or into another corporation
(other than a merger with another corporation in which the Company is the acquiring and the
surviving corporation and which does not result in any reclassification or change of
outstanding securities issuable upon exercise of this warrant), the Company, or such successor
or purchasing corporation, as the case may be, shall (i) in the case of a merger described
above, (A) if Shareholder Approval has not been obtained, deliver to the Holder cash in an
amount equal to the number of Shares multiplied by the difference between (x) the then-current
fair market value of the Shares and (y) the then-current Warrant Price, and (B) if Shareholder
Approval has been obtained, execute and deliver to the Holder a new warrant (in form and
substance reasonably satisfactory to the Holder), so that the Holder shall have the right to
receive upon exercise of this warrant, at a total purchase price equal to that payable upon
the exercise of the unexercised portion of this warrant, and in lieu of the shares of Common
Stock theretofore issuable upon exercise of this warrant, the kind and amount of shares of
stock, other securities, money and property receivable upon such merger or sale by a Holder of
the number of shares of Common Stock then purchasable under this warrant and (ii) in the case
of a reclassification or change in the securities issuable upon exercise of this warrant
described above, the Holder shall have the right to receive, upon exercise of this warrant, at
a total purchase price equal to that payable upon the exercise of the unexercised portion of
this warrant, and (A) in lieu of the shares of Common Stock theretofore issuable upon exercise
of this warrant, the number of shares of Common Stock then purchasable under this warrant upon
such reclassification or other change in the securities issuable upon exercise of this warrant
or (B) in lieu of cash theretofore issuable upon exercise of this warrant, the amount of cash
then issuable under this warrant upon such reclassification or other change in the securities
issuable upon exercise of this warrant. Any new warrant shall provide for adjustments that
shall be as nearly equivalent as may be practicable to the adjustments provided for in this
Section 4. The provisions of this Section 4(a) shall similarly apply to successive
reclassifications, changes, mergers and sales.

	(b)	 	Subdivision or Combination of Shares. If the Company at any time while this warrant
remains outstanding and unexpired shall subdivide or combine its outstanding shares of Common
Stock, the Warrant Price shall be proportionately decreased and the number of Shares issuable
hereunder shall be proportionately increased in the case of a subdivision and the Warrant
Price shall be proportionately increased and the number of Shares issuable hereunder shall be
proportionately decreased in the case of a combination.

	(c)	 	Stock Dividends and Other Distributions. If the Company at any time while this
warrant is outstanding and unexpired shall (i) pay a dividend with respect to Common Stock
payable in Common Stock, then the Warrant Price shall be adjusted, from and after the date of
determination of shareholders entitled to receive such dividend or distribution, to that price
determined by multiplying the Warrant Price in effect immediately prior to such date of
determination by a fraction (A) the numerator of which shall be the total number of shares of
Common Stock outstanding immediately prior to such dividend or distribution, and (B) the
denominator of which shall be the total number of shares of Common Stock outstanding
immediately after such dividend or distribution; or (ii) make any other distribution with
respect to Common Stock (except any distribution specifically provided for in Sections 4(a)
and 4(b)), then, in each such case, provision shall be made by the Company such that the
Holder of this warrant shall receive upon exercise of this warrant a proportionate share of
any such dividend or distribution as though it were the holder of the Common Stock as of the
record date fixed for the determination of the shareholders of the Company entitled to receive
such dividend or distribution.

	(d)	 	Adjustment of Number of Shares. Upon each adjustment in the Warrant Price, the
number of shares of Common Stock purchasable hereunder shall be adjusted, rounded up to the
nearest whole share, to the product obtained by multiplying the number of Shares purchasable
immediately prior to such adjustment in the Warrant Price by a fraction, the numerator of
which shall be the Warrant Price immediately prior to such adjustment and the denominator of
which shall be the Warrant Price immediately thereafter.

5. Notice of Adjustments. Whenever the Warrant Price or the number of Shares purchasable hereunder
shall be adjusted pursuant to Section 4 hereof, the Company shall make a certificate signed by its
acting chief financial officer setting forth, in reasonable detail, the event requiring the
adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and
the Warrant Price and the number of Shares purchasable hereunder after giving effect to such
adjustment, and shall cause copies of such certificate to be mailed to the Holder of this warrant.

6. Fractional Shares. In the event Shareholder Approval has been obtained and shares of Common
Stock are to be issued upon the exercise of this warrant, no fractional shares of Common Stock will
be issued in connection with any exercise hereunder, but in lieu of such fractional shares the
Company shall make a cash payment therefor based on the product resulting from multiplying the then
fair market value of the Common Stock on the date of exercise as determined in good faith by the
Company’s Board of Directors by such fraction.

7. Compliance with Act; Disposition of Warrant or Shares of Common Stock.

	(a)	 	Compliance with Act. The Holder of this warrant, by acceptance hereof, agrees that
this warrant, and the shares of Common Stock to be issued upon exercise hereof are being
acquired for investment and that such Holder will not offer, sell or otherwise dispose of this
warrant, or any shares of Common Stock except under circumstances which will not result in a
violation of the Securities Act of 1933, as amended (the “Securities Act”), or any
applicable state securities laws. Upon exercise of this warrant, unless the Shares being
acquired are registered under the Securities Act and any applicable state securities laws or
an exemption from such registration is available, the Holder hereof shall confirm in writing
that the shares of Common Stock so purchased are being acquired for investment and not with a
view toward distribution or resale in violation of the Securities Act and shall confirm such
other matters related thereto as may be reasonably requested by the Company. This warrant and
all shares of Common Stock issued upon exercise of this warrant (unless registered under the
Securities Act and any applicable state securities laws) shall be stamped or imprinted with a
legend in substantially the following form:

THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933,
AS AMENDED (THE “SECURITIES ACT”), OR ANY STATE SECURITIES LAWS. THE SECURITIES REPRESENTED
HEREBY MAY NOT BE TRANSFERRED UNLESS (I) SUCH SECURITIES HAVE BEEN REGISTERED FOR SALE
PURSUANT TO THE SECURITIES ACT, (II) SUCH SECURITIES MAY BE SOLD PURSUANT TO RULE 144(K) OR
(III) THE COMPANY HAS RECEIVED AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO IT THAT SUCH
TRANSFER MAY LAWFULLY BE MADE WITHOUT REGISTRATION UNDER THE SECURITIES ACT OR QUALIFICATION
UNDER APPLICABLE STATE SECURITIES LAWS.

Said legend shall be removed by the Company, upon the request of a Holder, at such time as
the restrictions on the transfer of the applicable security have terminated.

	(b)	 	Disposition of Warrant or Shares. This warrant and any shares of Common Stock
acquired pursuant to the exercise or conversion of this warrant may be transferred only
pursuant to a registration statement filed under the Securities Act or an exemption from such
registration. Subject to such restrictions, the Company shall transfer this warrant from time
to time upon the books to be maintained by the Company for that purpose, upon surrender
thereof for transfer properly endorsed or accompanied by appropriate instructions for transfer
and such other documents as may be reasonably required by the Company, including, if required
by the Company, an opinion of counsel to the effect that such transfer is exempt from the
registration requirements of the Securities Act to establish that such transfer is being made
in accordance with the terms hereof, and a new warrant shall be issued to the transferee and
the surrendered warrant shall be cancelled by the Company. Each certificate representing this
warrant or the shares of Common Stock thus transferred (except a transfer pursuant to Rule 144
or 144A) shall bear a legend as to the applicable restrictions on transferability in order to
ensure compliance with such laws, unless such legend is not required in order to ensure
compliance with such laws. The Company may issue stop transfer instructions to its transfer
agent in connection with such restrictions.

	(c)	 	Applicability of Restrictions. Neither any restrictions of any legend described in
this warrant nor the requirements of Section 7(b) above shall apply to any transfer of, or
grant of a security interest in, this warrant (or the Common Stock obtainable upon exercise
hereof) or any part hereof (i) to a partner of the Holder if the Holder is a partnership or to
a member of the Holder if the Holder is a limited liability company, (ii) to a partnership of
which the Holder is a partner or to a limited liability company of which the Holder is a
member, or (iii) to any affiliate of the Holder if the Holder is a corporation; provided,
however, in any such transfer, if applicable, the transferee shall on the Company’s request
agree in writing to be bound by the terms of this warrant as if an original Holder hereof.

8. Rights as Shareholders; Information. No Holder of this warrant, as such, shall be
entitled to vote or receive dividends or be deemed the holder of Common Stock issuable upon the
exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon
the Holder of this warrant, as such, any of the rights of a shareholder of the Company or any right
to vote for the election of directors or upon any matter submitted to shareholders at any meeting
thereof, or to receive notice of meetings, or to receive dividends or subscription rights or
otherwise until this warrant shall have been exercised and the Shares purchasable upon the exercise
hereof shall have become deliverable, as provided herein.

9.  Right to Convert Warrant into Stock: Net Issuance.

	(a)	 	Right to Convert. In addition to and without limiting the rights of the Holder under
the terms of this warrant, in the event Shareholder Approval has been obtained and shares of
Common Stock are to be issued upon the exercise of this warrant, the Holder shall have the
right to convert this warrant or any portion thereof (the “Conversion Right”) into
            shares of Common Stock as provided in this Section 9 at any time or from time to time during
the term of this warrant. Upon exercise of the Conversion Right with respect to a particular
number of shares subject to this warrant (the “Converted Warrant Shares”), the Company
shall deliver to the Holder (without payment by the Holder of any exercise price or any cash
or other consideration) that number of shares of fully paid and nonassessable Common Stock as
is determined according to the following formula:

X = (B – A) Divided by Y

Where: X = the number of shares of Common Stock that shall be issued to Holder

Y = the fair market value of one share of Common Stock

A = the aggregate Warrant Price of the specified number of Converted Warrant Shares immediately
prior to the exercise of the Conversion Right (i.e., the number of Converted Warrant Shares
multiplied by the Warrant Price)

B = the aggregate fair market value of the specified number of Converted Warrant Shares (i.e., the
number of Converted Warrant Shares multiplied by the fair market value of one Converted Warrant
Share)

If shares of Common Stock are issuable pursuant to this Section 9, no fractional shares shall be
issuable upon exercise of the Conversion Right, and, if the number of shares to be issued
determined in accordance with the foregoing formula is other than a whole number, the Company shall
pay to the Holder an amount in cash equal to the fair market value of the resulting fractional
share on the Conversion Date (as hereinafter defined).

	(b)	 	Method of Exercise. The Conversion Right may be exercised by the Holder by the
surrender of this warrant at the principal office of the Company together with a written
statement (which may be in the form of Exhibit A-1) specifying that the Holder thereby intends
to exercise the Conversion Right and indicating the number of shares subject to this warrant
which are being surrendered (referred to in Section 9(a) hereof as the Converted Warrant
Shares) in exercise of the Conversion Right. Such conversion shall be effective upon receipt
by the Company of this warrant together with the aforesaid written statement, or on such later
date as is specified therein (the “Conversion Date”). Certificates for the shares
issuable upon exercise of the Conversion Right and, if applicable, a new warrant evidencing
the balance of the shares remaining subject to this warrant, shall be issued as of the
Conversion Date and shall be delivered to the Holder within thirty (30) days following the
Conversion Date.

	(c)	 	Determination of Fair Market Value. For purposes of this Section 9, “fair market
value” of a share of Common Stock as of a particular date (the “Determination
Date”) shall mean: (i) if traded on a securities exchange, the fair market value of the
Common Stock shall be deemed to be the average of the closing prices of the Common Stock on
such exchange over the five trading days immediately prior to the Determination Date as
reported by Bloomberg Financial Markets (or a comparable reporting service of national
reputation selected by the Company and reasonably acceptable to the Holder if Bloomberg
Financial Markets is not then reporting sales prices of such security) (collectively,
“Bloomberg”); (ii) if traded on the Nasdaq Stock Market or other over-the-counter
system, the fair market value of the Common Stock shall be deemed to be the average of the
closing bid prices of the Common Stock over the five trading days immediately prior to the
Determination Date as reported by Bloomberg; and (iii) if there is no public market for the
Common Stock, then fair market value shall be determined by the Board of Directors of the
Company in good faith.

	(d)	 	Automatic Exercise: If this Warrant would terminate or expire but for the
application of this Section 9(d), then if the fair market value of one share of Common Stock
exceeds the Warrant Price this Warrant shall be deemed automatically converted pursuant to
this Section 9 immediately prior to such termination or expiration.

10. Representations and Warranties. The Company represents and warrants to the Holder of
this warrant as follows:

	(a)	 	This warrant has been duly authorized and executed by the Company and is a valid and binding
obligation of the Company enforceable in accordance with its terms, subject to laws of general
application relating to bankruptcy, insolvency and the relief of debtors and the rules of law
or principles at equity governing specific performance, injunctive relief and other equitable
remedies.

	(b)	 	The Shares have been duly authorized and reserved for issuance by the Company and, when
issued in accordance with the terms hereof, will be validly issued, fully paid and
nonassessable and free from preemptive rights.

	(c)	 	The execution and delivery of this warrant are not, and the issuance of the Shares upon
exercise of this warrant in accordance with the terms hereof will not be, inconsistent with
the Company’s articles of incorporation or bylaws, do not and will not contravene any law,
governmental rule or regulation, judgment or order applicable to the Company, and do not and
will not conflict with or contravene any provision of, or constitute a default under, any
indenture, mortgage, contract or other instrument of which the Company is a party or by which
it is bound or require the consent or approval of, the giving of notice to, the registration
or filing with or the taking of any action in respect of or by, any federal, state or local
government authority or agency or other person, except for the filing of notices pursuant to
federal and state securities laws, which filings will be effected by the time required
thereby.

11. Modification and Waiver. This warrant and any provision hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party against which
enforcement of the same is sought.

12. Notices. Any notice, request, communication or other document required or permitted to
be given or delivered to the Holder hereof or the Company shall be delivered, or shall be sent by
certified or registered mail, postage prepaid, to each such Holder at its address as shown on the
books of the Company or to the Company at the address indicated therefore on the signature page of
this warrant.

13. Binding Effect on Successors. This warrant shall be binding upon any corporation
succeeding the Company by merger, consolidation or acquisition of all or substantially all of the
Company’s assets, and all of the obligations of the Company relating to the Common Stock issuable
upon the exercise or conversion of this warrant shall survive the exercise, conversion and
termination of this warrant and all of the covenants and agreements of the Company shall inure to
the benefit of the successors and assigns of the Holder hereof.

14. Lost Warrants or Stock Certificates. The Company covenants to the Holder hereof that,
upon receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or
mutilation of this warrant or any stock certificate and, in the case of any such loss, theft or
destruction, upon receipt of an indemnity reasonably satisfactory to the Company, or in the case of
any such mutilation upon surrender and cancellation of such warrant or stock certificate, the
Company will make and deliver a new warrant or stock certificate, of like tenor, in lieu of the
lost, stolen, destroyed or mutilated warrant or stock certificate.

15. Descriptive Headings. The descriptive headings of the various sections of this warrant
are inserted for convenience only and do not constitute a part of this warrant. The language in
this warrant shall be construed as to its fair meaning without regard to which party drafted this
warrant.

16. Governing Law. This warrant shall be construed and enforced in accordance with, and
the rights of the parties shall be governed by, the laws of the State of Minnesota.

17. Remedies. In case any one or more of the covenants and agreements contained in this
warrant shall have been breached, the Holder hereof (in the case of a breach by the Company), or
the Company (in the case of a breach by the Holder), may proceed to protect and enforce their or
its rights either by suit in equity and/or by action at law, including, but not limited to, an
action for damages as a result of any such breach and/or an action for specific performance of any
such covenant or agreement contained in this warrant.

18. No Impairment of Rights. The Company will not, by amendment of its articles of
incorporation or through any other means, avoid or seek to avoid the observance or performance of
any of the terms of this warrant, but will at all times in good faith assist in the carrying out of
all such terms and in the taking of all such action as may be necessary or appropriate in order to
protect the rights of the Holder of this warrant against impairment.

19. Severability. The invalidity or unenforceability of any provision of this warrant in
any jurisdiction shall not affect the validity or enforceability of such provision in any other
jurisdiction, or affect any other provision of this warrant, which shall remain in full force and
effect.

20. Recovery of Litigation Costs. If any legal action or other proceeding is brought for
the enforcement of this warrant, or because of an alleged dispute, breach, default, or
misrepresentation in connection with any of the provisions of this warrant, the successful or
prevailing party or parties shall be entitled to recover reasonable attorneys’ fees and other costs
incurred in that action or proceeding, in addition to any other relief to which it or they may be
entitled.

21. Entire Agreement; Modification. This warrant constitutes the entire agreement between
the parties pertaining to the subject matter contained in it and supersedes all prior and
contemporaneous agreements, representations, and undertakings of the parties, whether oral or
written, with respect to such subject matter.

(Signature page follows)

1

The Company has caused this Warrant to be duly executed and delivered as of the Date of Grant
specified above.

ATS MEDICAL, INC.

	 
	By: /s/ Michael R. Kramer

Name: Michael R. Kramer

Title: Acting Chief Financial Officer

Address: 3905 Annapolis Lane North

Suite 105

Minneapolis, MN 55447

2

EXHIBIT A-1

NOTICE OF EXERCISE

To: ATS MEDICAL, INC. (the “Company”)

1. The undersigned hereby:

if Shareholder Approval has not been obtained as described in the warrant,
elects to receive cash upon the exercise of      shares of common
stock of the Company pursuant to the terms of the attached warrant,

if Shareholder Approval has been obtained as described in the warrant,
elects to purchase     shares of common stock of the Company pursuant to
the terms of the attached warrant, and tenders herewith payment of the
purchase price of such shares in full, or

if Shareholder Approval has been obtained as described in the warrant,
elects to exercise its net issuance rights pursuant to Section 9 of the
attached warrant with respect to     shares of common stock.

2. If Shareholder Approval has been obtained, please issue a certificate or certificates
representing      shares in the name of the undersigned or in such other name or names as are
specified below:

(Name)

(Address)

3. The undersigned represents that any aforesaid shares are being acquired for the account of the
undersigned for investment and not with a view to, or for resale in connection with, the
distribution thereof and that the undersigned has no present intention of distributing or reselling
such shares, all except as in compliance with applicable securities laws.

(Signature)

(Date)

3EX-10.5

EXHIBIT 10.5

REGISTRATION RIGHTS AGREEMENT

This Registration Rights Agreement (the “Agreement”) is made and entered into as of
this 28th day of June, 2007 by and among ATS Medical, Inc., a Minnesota corporation (the
“Company”), and the “Investors” named in that certain Common Stock and Warrant Purchase
Agreement, dated as of June 19, 2007 (the “Purchase Agreement”), by and among the Company
and the Investors.

The parties hereby agree as follows:

1. Certain Definitions.

As used in this Agreement, the following terms shall have the following meanings:

“Affiliate” means, with respect to any Person, any other Person which directly or
indirectly controls, is controlled by, or is under common control with, such Person.

“Business Day” means a day, other than a Saturday or Sunday, on which banks in New
York City are open for the general transaction of business.

“Common Stock” shall mean the Company’s common stock, par value $0.01 per share.

“Effectiveness Date” means the date on which any Registration Statement is declared
effective by the SEC.

“Exchange Act” means the Securities Exchange Act of 1934, as amended, and the rules
and regulations promulgated thereunder.

“Filing Date” means the date on which any Registration Statement is first filed with
the SEC.

“Filing Deadline” shall have the meaning set forth in Section 2(a) below.

“Investors” shall mean the Investors identified in the Purchase Agreement and any
Affiliate or permitted transferee of any Investor who is a subsequent holder of any Registrable
Securities.

“Person” means an individual, corporation, partnership, limited liability company,
trust, business trust, association, joint stock company, joint venture, sole proprietorship,
unincorporated organization, governmental authority or any other form of entity not specifically
listed herein.

“Prospectus” shall mean the prospectus included in any Registration Statement, as
amended or supplemented by any prospectus supplement, with respect to the terms of the offering of
any portion of the Registrable Securities covered by such Registration Statement and by all other
amendments and supplements to the prospectus, including post-effective amendments and all material
incorporated by reference in such prospectus.

“Register,” “registered” and “registration” refer to a registration
made by preparing and filing a Registration Statement or similar document in compliance with the
Securities Act (as defined below), and the declaration or ordering of effectiveness of such
Registration Statement or document.

“Registrable Securities” shall mean (i) the Shares, (ii) upon receipt of Shareholder
Approval, the Warrant Shares and (iii) any other securities issued or issuable with respect to or
in exchange for Shares and the Warrant Shares, including shares issued upon any stock split, stock
dividend, recapitalization, subdivision or similar event, provided that a security shall cease to
be a Registrable Security upon (A) sale pursuant to a Registration Statement or Rule 144 under the
Securities Act or (B) such security becoming eligible for sale by the Investors pursuant to Rule
144(k).

“Registration Statement” shall mean any registration statement of the Company filed
under the Securities Act that covers the resale of any of the Registrable Securities pursuant to
the provisions of this Agreement, amendments and supplements to such Registration Statement,
including post-effective amendments, all exhibits and all material incorporated by reference in
such Registration Statement.

“Required Investors” means the Investors holding a majority of the Registrable
Securities.

“SEC” means the Securities and Exchange Commission.

“Securities Act” means the Securities Act of 1933, as amended, and the rules and
regulations promulgated thereunder.

“Shares” means the shares of Common Stock issued pursuant to the Purchase Agreement.

“Shares Filing Deadline” shall have the meaning set forth in Section 2(a) below.

“Shares Registration Statement” shall have the meaning set forth in Section 2(a)
below.

“Shareholder Approval” means such approval as may be required by the applicable rules
and regulations of the Nasdaq Stock Market (or any successor entity) from the shareholders of the
Company in order to enable the Company to issue Common Stock (rather than cash) in connection with
the exercise of the Warrants.

“Shareholder Approval Date” means the date upon which the Company receives Shareholder
Approval.

“Warrant Shares” means the shares of Common Stock issuable upon exercise of the
Warrants following the receipt of Shareholder Approval.

“Warrant Shares Filing Deadline” shall have the meaning set forth in Section 2(a)
below.

“Warrant Shares Registration Statement” shall have the meaning set forth in Section
2(a) below.

“Warrants” means the Warrants issued pursuant to the Purchase Agreement.

2. Registration.

(a) Registration Statements. As soon as reasonably practicable following (i) the
Closing (as defined in the Purchase Agreement), but no later than thirty (30) days after the
Closing (the “Shares Filing Deadline”), the Company shall prepare and file with the SEC a
Registration Statement on Form S-3 (the “Shares Registration Statement”) covering the
resale of the Shares and (ii) the Shareholder Approval Date, but no later than thirty (30) days
after the Shareholder Approval Date (the “Warrant Shares Filing Deadline” and, together
with the Shares Filing Deadline, each a “Filing Deadline”), the Company shall prepare and
file with the SEC a Registration Statement on Form S-3 (the “Warrant Shares Registration
Statement” and, together with the Shares Registration Statement, each a “Registration
Statement”) covering the resale of the Warrant Shares; provided, however, that
if and to the extent that the Shares and the Warrant Shares may be included in a single
Registration Statement in accordance with the Securities Act and the rules and regulations
promulgated thereunder, the Company shall include the Shares and the Warrant Shares in the Shares
Registration Statement and shall file such Registration Statement in accordance with the terms and
time periods applicable to such Shares Registration Statement. The Registration Statement(s) also
shall cover, to the extent allowable under the Securities Act and the rules and regulations
promulgated thereunder, such indeterminate number of additional shares of Common Stock resulting
from stock splits, stock dividends or similar transactions with respect to the Shares. The
Registration Statement(s) (and each amendment or supplement thereto, and each request for
acceleration of effectiveness thereof) shall be provided in accordance with Section 3(c) to the
Investors and their counsel prior to its filing or other submission. If a Registration Statement
covering the Registrable Securities is not filed with the SEC on or prior to the applicable Filing
Deadline, the Company will make pro rata payments to each Investor, as liquidated damages and not
as a penalty, in an amount equal to one percent (1.0%) of the aggregate amount invested by such
Investor for each 30-day period or pro rata for any portion thereof following the applicable Filing
Deadline for which no Registration Statement is filed with respect to such Registrable Securities;
provided, however, that the aggregate amount of such liquidated damages payable to
each Investor, together with the amount of any liquidated damages previously paid pursuant to any
provision of this Agreement, shall under no circumstances exceed twelve percent (12%) of the
aggregate amount invested by such Investor. Such payments shall be made to each Investor in cash.

(b) Expenses. The Company will pay all expenses associated with each registration,
including filing and printing fees, the Company’s counsel and accounting fees and expenses, costs
associated with clearing the Registrable Securities for sale under applicable state securities laws
and listing fees, but excluding fees and expenses of counsel to the Investors, discounts,
commissions, fees of underwriters, selling brokers, dealer managers or similar securities industry
professionals with respect to the Registrable Securities being sold.

(c) Effectiveness.

(i) The Company shall use commercially reasonable efforts to have each Registration Statement
declared effective as soon as practicable. The Company shall notify the Investors by facsimile or
e-mail as promptly as practicable, and in any event, within twenty-four (24) hours, after any
Registration Statement is declared effective and shall provide the Investors with copies of any
related Prospectus to be used in connection with the sale or other disposition of the securities
covered thereby. If the Shares Registration Statement covering the Shares or the Warrant Shares
Registration Statement covering the Warrant Shares, as applicable, is not declared effective by the
SEC within (i) ninety (90) days after the applicable Filing Date if the SEC shall have informed the
Company that no review of such Registration Statement will be made or (ii) one hundred twenty (120)
days after such Filing Date if the SEC shall have informed the Company that a review of such
Registration Statement will be made, then the Company will make pro rata payments to each Investor,
as liquidated damages and not as a penalty, in an amount equal to one percent (1.0%) of the
aggregate amount invested by such Investor for each 30-day period or pro rata for any portion
thereof following the date by which such Registration Statement should have been effective;
provided, however, that the aggregate amount of such liquidated damages payable to
each Investor, together with the amount of any liquidated damages previously paid pursuant to any
provision of this Agreement, shall under no circumstances exceed twelve percent (12%) of the
aggregate amount invested by such Investor. Such payments shall be made to each Investor in cash.

(ii) The Company shall not file a registration statement on Form S-1 or Form S-3 until the
Effectiveness Date of the Shares Registration Statement.

3. Suspension.

(a) Subject to Section 3(b) below, in the event: (i) of any request by the SEC or any
other federal or state governmental authority during the period of effectiveness of any
Registration Statement for amendments or supplements to such Registration Statement or related
prospectus or for additional information so that such Registration Statement will not contain an
untrue statement of a material fact or omit to state a material fact required to be stated therein
or necessary to make the statements therein not misleading or otherwise fail to comply with the
applicable rules and regulations of the federal securities laws; (ii) of the issuance by the SEC or
any other federal or state governmental authority of any stop order suspending the effectiveness of
such Registration Statement or the initiation of any proceedings for that purpose; (iii) of the
receipt by the Company of any notification with respect to the suspension of the qualification or
exemption from qualification of any of the Registrable Securities for sale in any jurisdiction or
the initiation of any proceeding for such purpose, provided that, considering the advice of
counsel, the Company reasonably believes that it must qualify in such jurisdiction; (iv) of any
event or circumstance that, considering the advice of counsel, the Company reasonably believes
necessitates the making of any changes in such Registration Statement or related prospectus, or any
document incorporated or deemed to be incorporated therein by reference, so that, in the case of
such Registration Statement, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary to make the statements
therein not misleading, and that in the case of a related prospectus, it will not contain any
untrue statement of a material fact or any omission to state a material fact required to be stated
therein or necessary to make the statements therein, in the light of the circumstances under which
they were made, not misleading; or (v) that the Company reasonably believes, considering the advice
of counsel, that the Company may, in the absence of a suspension described hereunder, be required
under state or federal securities laws to disclose any corporate development, the disclosure of
which could reasonably be expected to have a material adverse effect upon the Company, its
shareholders, a potentially material transaction or event involving the Company, or any
negotiations, discussions or proposals directly relating thereto; then the Company shall deliver a
certificate in writing to each Holder of Registrable Securities (the “Suspension Notice”)
to the effect of the foregoing (but in no event, without the prior written consent of an Investor,
shall the Company disclose to such Investor any of the facts or circumstances regarding any
material nonpublic information) and, upon receipt of such Suspension Notice, the Holder will
refrain from selling any Registrable Securities pursuant to the Registration Statement (a
“Suspension”) until the Holder’s receipt of copies of a supplemented or amended prospectus
prepared and filed by the Company or until the Holder is advised in writing by the Company that the
current prospectus may be used and the Holder has received copies of any additional or supplemental
filings that are incorporated or deemed incorporated by reference in any such prospectus.

(b) Notwithstanding the foregoing, the Company shall not suspend any Registration Statement or
related prospectus for more than thirty (30) consecutive days or for a total of more than sixty
(60) days in any twelve (12) month period (each a “Permitted Suspension” and together the
“Permitted Suspensions”).

(c) On any day after the Effectiveness Date for the Shares Registration Statement or Warrant
Shares Registration Statement, as applicable, sales of such Registrable Securities as may be
required to be included on such Registration Statement cannot be made pursuant to such Registration
Statement (including, without limitation, because of a failure to keep such Registration Statement
effective, to disclose such information as is necessary for sales to be made pursuant to such
Registration Statement or to register sufficient shares of Registrable Securities or because of a
Suspension) then the Company will make pro rata payments to each Investor, as liquidated damages
and not as a penalty, in an amount equal to one percent (1.0%) of the aggregate amount invested by
such Investor for each 30-day period or pro rata for any portion thereof following the date by
which such sales of Registrable Securities under the Registration Statement cannot be made;
provided, however, that the aggregate amount of such liquidated damages payable to
each Investor, together with the amount of any liquidated damages previously paid pursuant to any
provision of this Agreement, shall under no circumstances exceed twelve percent (12%) of the
aggregate amount invested by such Investor. Such payments shall be made to each Investor in cash.
Notwithstanding the foregoing, the Company shall not be required to pay liquidated damages during
any Permitted Suspension.

(d) The Company will use commercially reasonable efforts to terminate an Suspension as
promptly as practicable after delivery of a Suspension Notice to the Holders.

4. Company Obligations. The Company will use commercially reasonable efforts to effect the
registration of the Registrable Securities in accordance with the terms hereof, and pursuant
thereto the Company will, as expeditiously as possible:

(a) cause each such Registration Statement to become effective and to remain continuously
effective for a period that will terminate upon the earlier of (i) the date on which all
Registrable Securities have been sold pursuant to the applicable Registration Statement, as such
Registration Statement may be amended from time to time, (ii) the date on which all Registrable
Securities covered by such Registration Statement may be sold pursuant to Rule 144 in a three-month
period and (iii) the two (2) year anniversary of the Effectiveness Date of such Registration
Statement (the “Effectiveness Period”) and advise the Investors in writing when the
applicable Effectiveness Period has expired;

(b) prepare and file with the SEC such amendments and post-effective amendments to each
Registration Statement and such supplements to the Prospectus as may be necessary to keep such
Registration Statement effective for the period specified in Section 4(a) and to comply with the
provisions of the Securities Act and the Exchange Act with respect to the distribution of all of
the Registrable Securities covered thereby;

(c) provide copies to and permit counsel designated by the Investors to review each
Registration Statement and any amendments or supplements thereto and any comments made by the staff
of the SEC and the Company’s responses thereto a reasonable period of time prior to its filing with
the SEC or its receipt from the SEC as applicable and shall duly consider comments made by such
counsel thereon;

(d) furnish to the Investors and their legal counsel (i) promptly after the same is prepared
and publicly distributed, filed with the SEC, or received by the Company (but not later than two
(2) Business Days after the filing date, receipt date or sending date, as the case may be) one (1)
copy of any Registration Statement and any amendment thereto, each preliminary prospectus, free
writing prospectus and Prospectus and each amendment or supplement thereto (as applicable), and
each letter written by or on behalf of the Company to the SEC or the staff of the SEC, and each
item of correspondence from the SEC or the staff of the SEC, in each case relating to such
Registration Statement (other than any portion of any thereof which contains information for which
the Company has sought confidential treatment), and (ii) an electronic copy of a Prospectus,
including a preliminary prospectus and any free writing prospectus, and all amendments and
supplements thereto and such other documents as each Investor may reasonably request in connection
with the disposition of such Registrable Securities owned by such Investor that are covered by the
related Registration Statement;

(e) use commercially reasonable efforts to (i) prevent the issuance of any stop order or other
suspension of effectiveness and, (ii) if such order is issued, obtain the withdrawal of any such
order at the earliest practicable time and to notify each Investor of the issuance of such an order
and the resolution thereof;

(f) prior to any public offering of Registrable Securities, use commercially reasonable
efforts to register or qualify or cooperate with the Investors and their counsel in connection with
the registration or qualification of such Registrable Securities for offer and sale under the
securities or blue sky laws of such jurisdictions requested by the Investors and do any and all
other commercially reasonable acts or things necessary or advisable to enable the distribution in
such jurisdictions of the Registrable Securities covered by such Registration Statement; provided,
however, that the Company shall not be required in connection therewith or as a condition thereto
to (i) qualify to do business in any jurisdiction where it would not otherwise be required to
qualify but for this Section 3(f), (ii) subject itself to general taxation in any jurisdiction
where it would not otherwise be so subject but for this Section 3(f), or (iii) file a general
consent to service of process in any such jurisdiction;

(g) use commercially reasonable efforts to cause all Registrable Securities covered by such
Registration Statement to be listed on each securities exchange, interdealer quotation system or
other market on which similar securities issued by the Company are then listed;

(h) immediately notify the Investors, at any time when a Prospectus relating to Registrable
Securities is required to be delivered under the Securities Act, upon discovery that, or upon the
happening of any event as a result of which, the Prospectus included in a Registration Statement,
as then in effect, includes an untrue statement of a material fact or omits to state any material
fact required to be stated therein or necessary to make the statements therein not misleading in
light of the circumstances then existing, and at the request of any such holder, promptly prepare
and furnish to such holder an electronic copy of a supplement to or an amendment of such Prospectus
as may be necessary so that, as thereafter delivered to the purchasers of such Registrable
Securities, such Prospectus shall not include an untrue statement of a material fact or omit to
state a material fact required to be stated therein or necessary to make the statements therein not
misleading in light of the circumstances then existing;

(i) otherwise use commercially reasonable efforts to comply with all applicable rules and
regulations of the SEC under the Securities Act and the Exchange Act, take such other actions as
may be reasonably necessary to facilitate the registration of the Registrable Securities hereunder;
and make available to its security holders, as soon as reasonably practicable, but not later than
the Availability Date (as defined below), an earnings statement covering a period of at least
twelve (12) months, beginning after the effective date of each Registration Statement, which
earnings statement shall satisfy the provisions of Section 11(a) of the Securities Act, including
Rule 158 promulgated thereunder (for the purpose of this subsection 3(i), “Availability
Date” means the 45th day following the end of the fourth fiscal quarter that includes the
effective date of such Registration Statement, except that, if such fourth fiscal quarter is the
last quarter of the Company’s fiscal year, “Availability Date” means the 90th day after the
end of such fourth fiscal quarter); and

(j) with a view to making available to the Investors the benefits of Rule 144 (or its
successor rule) and any other rule or regulation of the SEC that may at any time permit the
Investors to sell shares of Common Stock to the public without registration, the Company covenants
and agrees to: (i) make and keep public information available, as those terms are understood and
defined in Rule 144, during the applicable Effectiveness Period; (ii) file with the SEC in a timely
manner all reports and other documents required of the Company under the Exchange Act; and (iii)
furnish to each Investor upon request, as long as such Investor owns any Registrable Securities,
(A) a written statement by the Company that it has complied with the reporting requirements of the
Exchange Act, (B) a copy of the Company’s most recent Annual Report on Form 10-K or Quarterly
Report on Form 10-Q, and (C) such other information as may be reasonably requested in order to
avail such Investor of any rule or regulation of the SEC that permits the selling of any such
Registrable Securities without registration.

5. Obligations of the Investors.

(a) Each Investor shall furnish in writing to the Company such information regarding
itself, the Registrable Securities held by it and the intended method of disposition of the
Registrable Securities held by it, as shall be required to effect the registration of such
Registrable Securities and shall execute such documents in connection with such registration as the
Company may reasonably request. At least five (5) Business Days prior to the first anticipated
filing date of any Registration Statement, the Company shall notify each Investor of the
information the Company requires from such Investor if such Investor elects to have any of the
Registrable Securities included in the Registration Statement. An Investor shall provide such
information to the Company at least two (2) Business Days prior to the first anticipated filing
date of such Registration Statement if such Investor elects to have any of the Registrable
Securities included in the Registration Statement.

(b) Each Investor, by its acceptance of the Registrable Securities agrees to cooperate with
the Company as reasonably requested by the Company in connection with the preparation and filing of
a Registration Statement hereunder, unless such Investor has notified the Company in writing of its
election to exclude all of its Registrable Securities from such Registration Statement.

(c) Each Investor agrees that, upon receipt of any notice from the Company of either (i) the
commencement of a Suspension pursuant to Section 3, such Investor will immediately discontinue
disposition of Registrable Securities pursuant to any Registration Statement covering such
Registrable Securities, until the Investor’s receipt of the supplemented or amended prospectus
filed with the SEC and until any related post-effective amendment is declared effective and, if so
directed by the Company, the Investor shall deliver to the Company (at the expense of the Company)
or destroy (and deliver to the Company a certificate of destruction) all copies in the Investor’s
possession of the Prospectus covering the Registrable Securities current at the time of receipt of
such notice.

6. Indemnification.

(a) Indemnification by the Company. The Company agrees to indemnify and hold
harmless, to the fullest extent permitted by law, the Investors and their respective directors,
officers, employees, shareholders and each Person who controls any Investor (within the meaning of
the Securities Act) against any losses, claims, damages, liabilities and expense (including
reasonable attorneys’ fees) resulting from or which arise out of or are based up any untrue
statement or alleged untrue statement of a material fact or any omission or alleged omission of a
material fact required to be stated in any Registration Statement or Prospectus or preliminary
prospectus or free writing prospectus or amendment or supplement thereto or necessary to make the
statements therein not misleading and will reimburse each Investor and their respective directors,
officers, employees, shareholders or controlling Persons for any legal and other expenses
reasonably incurred as such expenses are reasonably incurred by such Person in connection with
investigating, defending, settling, compromising or paying any such loss, claim, damage, liability,
expense or action; provided, however, that the Company will not be liable in any such case if and
to the extent that any such loss, claim, damage or liability arises out of or is based upon an
untrue statement or alleged untrue statement or omission or alleged omission so made in conformity
with information furnished by an Investor in writing specifically for use in any such Registration
Statement or Prospectus or preliminary prospectus or free writing prospectus.

(b) Indemnification by the Investors. Each Investor agrees, severally but not
jointly, to indemnify and hold harmless, to the fullest extent permitted by law, the Company, its
directors, officers, employees, shareholders and each Person who controls the Company (within the
meaning of the Securities Act) against any losses, claims, damages, liabilities and expense
(including reasonable attorneys’ fees) resulting from or which arise out of or are based upon any
untrue statement or alleged untrue statement of a material fact or any omission or alleged omission
of a material fact required to be stated in any Registration Statement or Prospectus or preliminary
prospectus or free writing prospectus or amendment or supplement thereto or necessary to make the
statements therein not misleading, to the extent, but only to the extent that such untrue statement
or omission or alleged statement or omission is contained in any information furnished in writing
by such Investor to the Company specifically for inclusion in such Registration Statement or
Prospectus or free writing prospectus or amendment or supplement thereto, and will reimburse the
Company and its directors, officers, employees, shareholders or controlling Persons for any legal
and other expenses reasonably incurred as such expenses are reasonably incurred by such Person in
connection with investigating, defending, settling, compromising or paying any such loss, claim,
damage, liability, expense or action. In no event shall the liability of an Investor be greater in
amount than the dollar amount of the proceeds (net of all expense paid by such Investor in
connection with any claim relating to this Section 6 and the amount of any damages such Investor
has otherwise been required to pay by reason of such untrue statement or omission or alleged untrue
statement or omission) received by such Investor upon the sale of the Registrable Securities
included in any such Registration Statement giving rise to such indemnification obligation.

(c) Conduct of Indemnification Proceedings. Any Person entitled to indemnification
hereunder shall (i) give prompt notice to the indemnifying party of any claim with respect to which
it seeks indemnification and (ii) permit such indemnifying party to assume the defense of such
claim with counsel reasonably satisfactory to the indemnified party; provided that any
Person entitled to indemnification hereunder shall have the right to employ separate counsel and to
participate in the defense of such claim, but the fees and expenses of such counsel shall be at the
expense of such Person unless (a) the indemnifying party has agreed to pay such fees or expenses,
or (b) the indemnifying party shall have failed to assume the defense of such claim within five (5)
Business Days after written notice thereof and employ counsel reasonably satisfactory to such
Person or (c) in the reasonable judgment of any such Person, considering the advice of counsel, a
conflict of interest exists between such Person and the indemnifying party with respect to such
claims (in which case, if the Person notifies the indemnifying party in writing that such Person
elects to employ separate counsel at the expense of the indemnifying party, the indemnifying party
shall not have the right to assume the defense of such claim on behalf of such Person); and
provided, further, that the failure of any indemnified party to give notice as provided herein
shall not relieve the indemnifying party of its obligations hereunder, except to the extent that
such failure to give notice shall materially adversely affect the indemnifying party in the defense
of any such claim or litigation. It is understood that the indemnifying party shall not, in
connection with any proceeding in the same jurisdiction, be liable for fees or expenses of more
than one additional firm of attorneys at any time for all such indemnified parties. No
indemnifying party will, except with the consent of the indemnified party, consent to entry of any
judgment or enter into any settlement that does not include as an unconditional term thereof the
giving by the claimant or plaintiff to such indemnified party of a release from all liability in
respect of such claim or litigation.

(d) Contribution. If for any reason the indemnification provided for in the preceding
paragraphs (a) and (b) is unavailable to an indemnified party or insufficient to hold it harmless,
other than as expressly specified therein, then the indemnifying party shall contribute to the
amount paid or payable by the indemnified party as a result of such loss, claim, damage or
liability in such proportion as is appropriate to reflect the relative fault of the indemnified
party and the indemnifying party, as well as any other relevant equitable considerations. No
Person guilty of fraudulent misrepresentation within the meaning of Section 11(f) of the Securities
Act shall be entitled to contribution from any Person not guilty of such fraudulent
misrepresentation. In no event shall the contribution obligation of a holder of Registrable
Securities be greater in amount than the dollar amount of the proceeds (net of all expenses paid by
such holder in connection with any claim relating to this Section 6 and the amount of any damages
such holder has otherwise been required to pay by reason of such untrue or alleged untrue statement
or omission or alleged omission) received by it upon the sale of the Registrable Securities giving
rise to such contribution obligation.

7. Miscellaneous.

(a) Amendments and Waivers. This Agreement may be amended only by a writing
signed by the Company and the Required Investors. The Company may take any action herein
prohibited, or omit to perform any act herein required to be performed by it, only if the Company
shall have obtained the written consent to such amendment, action or omission to act, of the
Required Investors.

(b) Notices. All notices and other communications provided for or permitted hereunder
shall be made as set forth in Section 9.4 of the Purchase Agreement.

(c) Assignments and Transfers by Investors. The provisions of this Agreement shall be
binding upon and inure to the benefit of the Investors and their respective successors and assigns.
An Investor may transfer or assign, in whole or from time to time in part, to one or more Persons
its rights hereunder in connection with the transfer of Registrable Securities by such Investor to
such Person, provided that such Investor complies with all laws applicable thereto and
provides written notice of assignment to the Company promptly after such assignment is effected.

(d) Assignments and Transfers by the Company. This Agreement may not be assigned by
the Company (whether by operation of law or otherwise) without the prior written consent of the
Required Investors, provided, however, that the Company may assign its rights and
delegate its duties hereunder to any surviving or successor corporation in connection with a merger
or consolidation of the Company with another corporation, or a sale, transfer or other disposition
of all or substantially all of the Company’s assets to another corporation, without the prior
written consent of the Required Investors, after notice duly given by the Company to each Investor.

(e) Benefits of the Agreement. The terms and conditions of this Agreement shall inure
to the benefit of and be binding upon the respective permitted successors and assigns of the
parties. Nothing in this Agreement, express or implied, is intended to confer upon any party other
than the parties hereto or their respective successors and assigns any rights, remedies,
obligations, or liabilities under or by reason of this Agreement, except as expressly provided in
this Agreement.

(f) Counterparts; Faxes. This Agreement may be executed in two or more counterparts,
each of which shall be deemed an original, but all of which together shall constitute one and the
same instrument. This Agreement may also be executed via facsimile, which shall be deemed an
original.

(g) Titles and Subtitles. The titles and subtitles used in this Agreement are used
for convenience only and are not to be considered in construing or interpreting this Agreement.

(h) Severability. Any provision of this Agreement that is prohibited or unenforceable
in any jurisdiction shall, as to such jurisdiction, be ineffective to the extent of such
prohibition or unenforceability without invalidating the remaining provisions hereof but shall be
interpreted as if it were written so as to be enforceable to the maximum extent permitted by
applicable law, and any such prohibition or unenforceability in any jurisdiction shall not
invalidate or render unenforceable such provision in any other jurisdiction. To the extent
permitted by applicable law, the parties hereby waive any provision of law which renders any
provisions hereof prohibited or unenforceable in any respect.

(i) Further Assurances. The parties shall execute and deliver all such further
instruments and documents and take all such other actions as may reasonably be required to carry
out the transactions contemplated hereby and to evidence the fulfillment of the agreements herein
contained.

(j) Entire Agreement. This Agreement is intended by the parties as a final expression
of their agreement and intended to be a complete and exclusive statement of the agreement and
understanding of the parties hereto in respect of the subject matter contained herein. This
Agreement supersedes all prior agreements and understandings between the parties with respect to
such subject matter.

(k) Governing Law; Consent to Jurisdiction; Waiver of Jury Trial. This Agreement
shall be governed by, and construed in accordance with, the internal laws of the State of New York
without regard to the choice of law principles thereof. Each of the parties hereto irrevocably
submits to the exclusive jurisdiction of the courts of the State of New York located in New York
County and the United States District Court for the Southern District of New York for the purpose
of any suit, action, proceeding or judgment relating to or arising out of this Agreement and the
transactions contemplated hereby. Service of process in connection with any such suit, action or
proceeding may be served on each party hereto anywhere in the world by the same methods as are
specified for the giving of notices under this Agreement. Each of the parties hereto irrevocably
consents to the jurisdiction of any such court in any such suit, action or proceeding and to the
laying of venue in such court. Each party hereto irrevocably waives any objection to the laying of
venue of any such suit, action or proceeding brought in such courts and irrevocably waives any
claim that any such suit, action or proceeding brought in any such court has been brought in an
inconvenient forum. EACH OF THE PARTIES HERETO WAIVES ANY RIGHT TO REQUEST A TRIAL BY JURY IN ANY
LITIGATION WITH RESPECT TO THIS AGREEMENT AND REPRESENTS THAT COUNSEL HAS BEEN CONSULTED
SPECIFICALLY AS TO THIS WAIVER.

1

IN WITNESS WHEREOF, the parties have executed this Registration Rights Agreement as of the
date first above written.

The Company:

ATS MEDICAL, INC.

	 
	By: /s/ Michael R. Kramer

Name: Michael R. Kramer

Title: Acting Chief Financial Officer

The Investors:

ALTA PARTNERS VIII, L.P.

By: Alta Partners Management VIII, LLC

Its: General Partner

By: /s/ Hilary Strain

Name: Hilary Strain

Title: Chief Financial Officer

2

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