Exhibit 99.2

                    Certification of Chief Financial Officer
                         Pursuant to Section 906 of the
                           Sarbanes-Oxley Act of 2002

In connection with this quarterly report on Form 10-Q of Urologix, Inc. I,
Christopher R. Geyen, Chief Financial Officer of Urologix, Inc., certify,
pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that:

     .    The report fully complies with the requirements of Section 13(a) or
          15(d) of the Securities Exchange Act of 1934; and

     .    The information contained in this report fairly presents, in all
          material respects, the financial condition and results of operations
          of Urologix, Inc.

Date:  November 13, 2002               /s/ Christopher R. Geyen
                                       -----------------------------------------
                                       Christopher R. Geyen
                                       Vice President and
                                       Chief Financial Officer