<PAGE>
                                                                    EXHIBIT 10.1

                                    AMENDMENT
                                       TO
                           LOAN AND SECURITY AGREEMENT

     THIS AMENDMENT to Loan and Security Agreement (this "Amendment") is entered
into this 29th day of March, 2006, by and between Silicon Valley Bank ("Bank")
and each of ATS Medical, Inc., a Minnesota corporation (the "Borrower") whose
address is 3905 Annapolis Lane, Suite 105, Minneapolis, Minnesota 55447.

                                    RECITALS

     A. Bank and Borrower have entered into that certain Loan and Security
Agreement dated as of July 28, 2004 (as amended, modified, supplemented or
restated from time to time, the "Loan Agreement").

     B. Bank has extended credit to Borrower for the purposes permitted in the
Loan Agreement.

     C. Borrower has requested that Bank amend the Loan Agreement to (i)
increase the amount available to be borrowed under the Revolving Line, (ii)
extend the maturity date, (iii) add an additional equipment loan, and (iv) make
certain other revisions to the Loan Agreement as more fully set forth herein.

     D. Bank has agreed to so amend certain provisions of the Loan Agreement,
but only to the extent, in accordance with the terms, subject to the conditions
and in reliance upon the representations and warranties set forth below.

                                    AGREEMENT

     NOW, THEREFORE, in consideration of the foregoing recitals and other good
and valuable consideration, the receipt and adequacy of which is hereby
acknowledged, and intending to be legally bound, the parties hereto agree as
follows:

     1. DEFINITIONS. Capitalized terms used but not defined in this Amendment
shall have the meanings given to them in the Loan Agreement.

     2. CONSENT AND AMENDMENTS TO LOAN AGREEMENT.

        2.1 CONSENT TO ACQUISITION. Borrower has advised Bank that Borrower
intends to acquire all of the outstanding capital stock of 3F Therapeutics
pursuant to a Stock Purchase Agreement, or similar agreement, in exchange for
the issuance by Borrower of 9,000,000 shares of common stock of Borrower (the
"Acquisition"). As a result of the Acquisition, 3F Therapeutics will become a
wholly-owned subsidiary of Borrower. Pursuant to Section 7.3 of the Loan
Agreement, Borrower is prohibited from entering into the Acquisition absent
compliance with the terms set forth therein. Bank and Borrower hereby agree that
the prohibition set forth in Section 7.3 of the Loan Agreement is hereby waived
with respect to the Acquisition only and Bank hereby consents to the Acquisition
conditioned upon the following


                                      -1-


<PAGE>

requirements: (i) the conditions precedent (for Borrower and Sellers) set forth
in the Stock Purchase Agreement, or similar agreement, are satisfied; (ii) no
Default or Event of Default has occurred and is continuing at the time of, or
would occur as a result of, the Acquisition; and (iii) the assets of 3F
Therapeutics are free and clear of all liens. Nothing herein is to be deemed a
waiver of Bank's right to require that 3F Therapeutics be made a co-Borrower
under the Loan Agreement or a guarantor of the Obligations thereunder and to
require 3F Therapeutics to execute documents related thereto. It is further
understood by the parties hereto that such waiver and consent shall in no way be
construed as commitment or agreement by Bank to provide any financing
arrangements with or for Borrower with respect to the Acquisition. It is also
further understood by the parties hereto that such waiver does not constitute a
waiver of any other provision or term of the Loan Agreement or any related
document, nor an agreement by the Bank to waive in the future this covenant or
any other provision or term of the Loan Agreement or any related document.

     2.2 UPDATED FINANCIAL STATEMENTS. Borrower shall provide Bank with updated
financial statements by June 1, 2006, which financial statements will reflect
the impact of the Acquisition. The Tangible Net Worth financial covenant will
then be reset based upon such updated financial statements.

     2.3 NEW EQUIPMENT ADVANCES. Section 2.1.6 is amended in its entirety and
replaced with the following:

         SECTION 2.1.6 NEW EQUIPMENT ADVANCES.

                    (a) At Borrower's request made pursuant to subsection (c)
               below on or before March 30, 2006, Bank will make an advance of
               $1,500,000 (the "New Equipment Advance"). The New Equipment
               Advance may only be used to finance or refinance Eligible
               Equipment purchased on or after June 1, 2005 and on or before May
               31, 2006 ("New Equipment Advance Eligible Equipment").
               Concurrently herewith, Borrower shall deliver to Bank copies of
               all invoices for New Equipment Advance Eligible Equipment that
               will be financed by the New Equipment Advance that has been
               purchased prior to the date hereof, and going forward Borrower
               shall deliver to Bank copies of all invoices for New Equipment
               Advance Eligible Equipment that will be financed by the New
               Equipment Advance that has been purchased on or after the date
               hereof immediately after such purchase. If on June 30, 2006 the
               outstanding amount of the New Equipment Advance exceeds the
               aggregate Eligible Equipment Invoice Amounts for which Borrower
               has provided Bank with invoices, then Borrower shall immediately
               pay the amount of such excess (the "Excess New Equipment
               Advance") to Bank. As used herein, "Eligible Equipment Invoice
               Amount" shall mean 100% of the New Equipment Advance Eligible
               Equipment on the invoice excluding taxes, shipping, warranty
               charges, freight discounts and installation expense, provided
               that software licenses, leasehold improvements and other soft



                                      -2-

<PAGE>

               costs may constitute up to but not exceed 25% of the aggregate
               Eligible Equipment Invoice Amounts.

                    (b) Interest accrues from the date of the New Equipment
               Advance at the rate in Section 2.3(a) and is payable monthly. For
               the first six months after the date of the New Equipment Advance
               (the "New Equipment Advance Date"), Borrower will pay interest
               only. Thereafter, the New Equipment Advance will be payable in 60
               equal monthly installments of principal, plus accrued interest,
               commencing on the date that is six months after the New Equipment
               Advance Date and continuing on the same date of each month
               thereafter until the date that is five years thereafter (the "New
               Equipment Advance Maturity Date"), on which date all remaining
               principal and accrued interest shall be paid in full. Once
               repaid, no portion of the New Equipment Advance may be
               reborrowed.

                    (c) To obtain the New Equipment Advance, Borrower must
               notify Bank (the notice is irrevocable) by facsimile no later
               than 2:00 p.m. Pacific time 1 Business Day before the day on
               which the New Equipment Advance is to be made. The notice in the
               form of Exhibit B (Payment/Advance Form) must be signed by a
               Responsible Officer or designee and include copies of the
               invoices for that portion of the Equipment being financed that
               was purchased prior to the date of the New Equipment Loan
               Advance.

                    (d) If Borrower shall pay all or any portion of the New
               Equipment Advance prior to its due date, or if all or any portion
               of the New Equipment Advance is declared due and payable prior to
               its due date as a result of an Event of Default, then Borrower
               shall pay Bank a fee with respect to each such prepaid or
               accelerated amount equal to 1% of said amount. The foregoing fee
               shall not be charged with respect to a prepayment that results
               from the replacement of the New Equipment Advance with a new
               facility from another division of the Bank, provided that no
               Event of Default then exists.

     2.4 MAXIMUM AGGREGATE ADVANCES. Section 2.1.7 is amended in its entirety
and replaced with the following:

         SECTION 2.1.7 MAXIMUM AGGREGATE ADVANCES. Not-withstanding anything
         herein to the contrary, in no event shall the aggregate amount of
         outstanding Revolving Advances, Equipment Advances and New Equipment
         Advances exceed $8,600,000.

     2.5 MODIFIED INTEREST RATE. Section 2.3(a) is amended in its entirety and
replaced with the following:


                                      -3-


<PAGE>

                    (a) Interest Rate. (i) Revolving Advances accrue interest on
               the outstanding principal balance at a per annum rate of 1.0
               percentage points above the Prime Rate, but in no event less than
               5.25% per annum; and (ii) Equipment Advances accrue interest on
               the outstanding principal balance at a per annum rate of 1.50
               percentage points above the Prime Rate, but in no event less than
               5.75% per annum; and (iii) New Equipment Advances accrue interest
               on the outstanding principal balance at a per annum rate of 1.75
               percentage points above the Prime Rate. After an Event of Default
               has occurred and while it is continuing, Obligations accrue
               interest at five (5) percentage points above the rate effective
               immediately before the Event of Default. The interest rate
               increases or decreases when the Prime Rate changes. Interest is
               computed on a 360 day year for the actual number of days elapsed.

     2.6 MODIFIED FINANCIAL COVENANTS. Section 6.7 is amended in its entirety
and replaced with the following:

         6.7 FINANCIAL COVENANTS.

             Borrower will maintain at all times, on a consolidated basis:

             (i) LIQUIDITY RATIO. A ratio of (y) unrestricted cash (and
             equivalents) of Borrower on deposit with Bank plus Borrower's
             Eligible Accounts, (z) divided by Current Liabilities, of equal
             to or greater than 2.0 to 1.00.

             (ii) TANGIBLE NET WORTH. A Tangible Net Worth, at the end of each
             month, of at least $40,000,000.

     2.7 MODIFIED DEFINITIONS. The following terms and their respective
definitions set forth in SECTION 13.1 are amended in their entirety and replaced
with the following:

             "COMMITTED REVOLVING LINE" is an aggregate of Credit Extensions
             of up to $8,000,000.

             "ELIGIBLE ACCOUNTS" are Accounts in the ordinary course of
             Borrower's business that meet all Borrower's representations and
             warranties in Section 5; but Bank may change eligibility
             standards for the reasons given in a written notice to Borrower.
             Unless Bank agrees otherwise in writing, Eligible Accounts will
             not include:


                                      -4-

<PAGE>


          (a) Accounts that the account debtor has not paid within 120 days of
          invoice date;

          (b) Accounts for an account debtor, 50% or more of whose Accounts have
          not been paid within 120 days of invoice date;

          (c) Credit balances over 120 days from invoice date;

          (d) Accounts for an account debtor, including Affiliates, whose total
          obligations to Borrower exceed 25% of all Accounts, for the amounts
          that exceed that percentage, unless the Bank approves in writing;

          (e) [Omitted];

          (f) Accounts for which the account debtor is a federal, state or local
          government entity or any department, agency, or instrumentality,
          unless Borrower has complied with the Assignments of Claim Act or
          comparable statute or ordinance, if required from such government
          entity, department, agency or instrumentality in order for a security
          interest in such Accounts to be enforceable or perfected, or for Bank
          to be able to enforce collection of such Accounts directly from such
          account debtor;

          (g) Accounts owed to an account debtor to which Borrower is obligated,
          but only up to the amount owed (sometimes called "contra" accounts,
          accounts payable, customer deposits or credit accounts);

          (h) Accounts for demonstration or promotional equipment, or in which
          goods are consigned, sales guaranteed, sale or return, sale on
          approval, bill and hold, or other terms if account debtor's payment
          may be conditional;

          (i) Accounts for which the account debtor is Borrower's Affiliate,
          officer, employee, or agent;

          (j) Accounts in which the account debtor disputes liability or makes
          any claim and Bank believes there may be a basis for dispute (but only
          up to the disputed or claimed amount), or if the Account Debtor is
          subject to an Insolvency Proceeding, or becomes insolvent, or goes out
          of business; and

          (k) Accounts for which Bank reasonably determines collection to be
          doubtful.

          "REVOLVING MATURITY DATE" is March 28, 2007 [the date that is 364 days
          from the date of this Amendment].


                                      -5-


<PAGE>

     3. LIMITATION OF AMENDMENTS.

        3.1 The amendments set forth in SECTION 2, above, are effective for
the purposes set forth herein and shall be limited precisely as written and
shall not be deemed to (a) be a consent to any amendment, waiver or modification
of any other term or condition of any Loan Document, or (b) otherwise prejudice
any right or remedy which Bank may now have or may have in the future under or
in connection with any Loan Document.

        3.2 This Amendment shall be construed in connection with and as part
of the Loan Documents and all terms, conditions, representations, warranties,
covenants and agreements set forth in the Loan Documents, except as herein
amended, are hereby ratified and confirmed and shall remain in full force and
effect.

     4. REPRESENTATIONS AND WARRANTIES. To induce Bank to enter into this
Amendment, Borrower hereby represents and warrants to Bank as follows:

        4.1 Immediately after giving effect to this Amendment (a) the
representations and warranties contained in the Loan Documents are true,
accurate and complete in all material respects as of the date hereof (except to
the extent such representations and warranties relate to an earlier date, in
which case they are true and correct as of such date), and (b) no Event of
Default has occurred and is continuing;

        4.2 Borrower has the power and authority to execute and deliver this
Amendment and to perform its obligations under the Loan Agreement, as amended by
this Amendment;

        4.3 The organizational documents of Borrower delivered to Bank on the
Effective Date remain true, accurate and complete and have not been amended,
supplemented or restated and are and continue to be in full force and effect;

        4.4 The execution and delivery by Borrower of this Amendment and the
performance by Borrower of its obligations under the Loan Agreement, as amended
by this Amendment, have been duly authorized;

        4.5 The execution and delivery by Borrower of this Amendment and the
performance by Borrower of its obligations under the Loan Agreement, as amended
by this Amendment, do not and will not contravene (a) any law or regulation
binding on or affecting Borrower, (b) any contractual restriction with a Person
binding on Borrower, (c) any order, judgment or decree of any court or other
governmental or public body or authority, or subdivision thereof, binding on
Borrower, or (d) the organizational documents of Borrower;

        4.6 The execution and delivery by Borrower of this Amendment and the
performance by Borrower of its obligations under the Loan Agreement, as amended
by this Amendment, do not require any order, consent, approval, license,
authorization or validation of, or filing, recording or registration with, or
exemption by any governmental


                                      -6-



<PAGE>

or public body or authority, or subdivision thereof, binding on either Borrower,
except as already has been obtained or made; and

        4.7 This Amendment has been duly executed and delivered by Borrower
and is the binding obligation of Borrower, enforceable against Borrower in
accordance with its terms, except as such enforceability may be limited by
bankruptcy, insolvency, reorganization, liquidation, moratorium or other similar
laws of general application and equitable principles relating to or affecting
creditors' rights.

     5. COUNTERPARTS. This Amendment may be executed in any number of
counterparts and all of such counterparts taken together shall be deemed to
constitute one and the same instrument.

     6. EFFECTIVENESS. This Amendment shall be deemed effective upon (a) the due
execution and delivery to Bank of this Amendment by each party hereto, and (b)
Borrower's payment of an amendment fee in an amount equal to $28,667.

                            [Signature page follows.]


                                      -7-


<PAGE>


     IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be
duly executed and delivered as of the date first written above.



BANK                                      BORROWER

Silicon Valley Bank                       ATS Medical, Inc.


By: /s/ Charles Roehl                     By: /s/ John R. Judd
Name:   Charles Roehl                     Name:   John R. Judd
        --------------------------                --------------------------
Title:  VP -- Relationship Manager        Title:  Chief Financial Officer
        --------------------------                --------------------------



                                      -8-