<PAGE>
 
As filed with the Securities and Exchange Commission on October 1, 1996
                                                 Registration No. 333- _________
--------------------------------------------------------------------------------

                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549
                         ____________________________

                                   FORM S-8
                            REGISTRATION STATEMENT
                                     UNDER
                          THE SECURITIES ACT OF 1933


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

                MINNESOTA                                     41-1697237
      ------------------------------                        -------------------
     (State or other jurisdiction of                         (I.R.S. Employer
      incorporation or organization)                        Identification No.)

                            14405 21ST AVENUE NORTH
                            MINNEAPOLIS, MN   55447
               ------------------------------------------------
             (Address of Principal Executive Offices and zip code)
                       _________________________________

                                UROLOGIX, INC.
                       1996 EMPLOYEE STOCK PURCHASE PLAN
                           (Full title of the Plan)
                         ____________________________
                               Wesley E. Johnson
                                   Secretary
                                Urologix, Inc.
                            14405 21st Avenue North
                            Minneapolis, MN   55447
                                (612) 475-1400
 (Name, address, including zip code and telephone number of agent for service)

                                   Copy to:

                           Thomas G. Lovett IV, Esq.
                          Lindquist & Vennum P.L.L.P.
                                4200 IDS Center
                            80 South Eighth Street
                            Minneapolis, MN  55402
                                (612) 371-3211
                          ___________________________
<PAGE>
 
                        CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION> 
--------------------------------------------------------------------------------------------
 
                                               Proposed
                       Proposed Maximum         Maximum                          Amount of
 Title of Securities     Amount to be     Offering Price Per      Aggregate     Registration
  to be Registered        Registered             Share         Offering Price       Fee
 
--------------------------------------------------------------------------------------------
<S>                    <C>                <C>                  <C>              <C>
 
Common Stock,             
$.01 par value
  Total                   100,000 shares        15.375(1)          $1,537,500    $       466
                                                                   ==========      =========
--------------------------------------------------------------------------------------------
</TABLE>

  (1)  Estimated solely for the purpose of determining the registration fee
       pursuant to Rule 457(c) and (h) and based upon the average of the bid and
       asked prices of the Company's Common Stock on the Nasdaq System at the
       close of business on September 30, 1996.

  
                                       2
<PAGE>
 
                                    PART II

Item 3.   Incorporation of Documents by Reference.
------------------------------------------------- 

          The following documents filed with the Securities and Exchange
Commission are hereby incorporated by reference herein:
          
          (a) Form 10-K Annual Report of the Company for the fiscal year ended
June 30, 1996.
          
          (b) Form 8-A Registration Statement, as amended, filed with the
Securities and Exchange Commission and declared effective May 29, 1996 under
File No. 0-28414.

          All documents subsequently filed by the Company pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934, prior to the
filing of a post-effective amendment which indicates that all securities offered
have been sold or which deregisters all securities then remaining unsold, shall
be deemed to be incorporated by reference in this Registration Statement and to
be a part hereof from the date of filing of such documents.

Item 4.   Description of Securities.
-----------------------------------

          Not applicable.

Item 5.   Interests of Named Experts and Counsel.
------------------------------------------------ 

          Not applicable.

Item 6.   Indemnification of Directors and Officers.
--------------------------------------------------- 

          The Company's Bylaws and the statutes of the State of Minnesota
require the Company to indemnify any director, officer, employee or agent who
was or is a party to any threatened, pending or completed action, suit or
proceeding, whether civil, criminal, administrative or investigative, against
certain liabilities and expenses incurred in connection with the action, suit or
proceeding, except where such persons have not acted in good faith or did not
reasonably believe that the conduct was in the best interests of the Company.

          Insofar as indemnification for liabilities arising under the
Securities Act of 1933, as amended (the "Securities Act"), may be permitted to
directors, officers or other persons controlling the Company pursuant to the
foregoing provisions, the Company has been informed that in the opinion of the
Securities and Exchange Commission (the "Commission"), such indemnification is
against public policy as expressed in the Securities Act and is therefore
unenforceable.

Item 7.   Exemption from Registration Claimed.
--------------------------------------------- 

          Not Applicable.


                                       3
<PAGE>
 
Item 8.  Exhibits.
----------------- 

     4.1    Urologix, Inc. 1996 Employee Stock Purchase Plan
     5.1    Opinion and Consent of Lindquist & Vennum P.L.L.P.
     23.1   Consent of Lindquist & Vennum (included in Exhibit 5)
     23.2   Consent of Arthur Andersen, LLP, Certified Public Accountants
_____________________

Item 9.  Undertakings.
--------------------- 

(a)  The undersigned registrant hereby undertakes:

     (1)  To file, during any period in which offers or sales are being made, a
post-effective amendment to this registration statement:

          (i)   To include any prospectus required by Section 10(a)(3) of the
     Securities Act of 1933;

          (ii)  To reflect in the prospectus any facts or events arising after
     the effective date of the registration statement (or the most recent post-
     effective amendment thereof) which, individually or in the aggregate,
     represent a fundamental change in the information set forth in the
     registration statement. Notwithstanding the foregoing, any increase or
     decrease in volume of securities offered (if the total dollar value of
     securities offered would not exceed that which was registered) and any
     deviation from the low or high end of the estimated maximum offering range
     may be reflected in the form of prospectus filed with the Commission
     pursuant to Rule 424(b) if, in the aggregate, the changes in volume and
     price represent no more than a 20% change in the maximum aggregate offering
     price set forth in the "Calculation of Registration Fee" table in the
     effective registration statement;

          (iii) To include any material information with respect to the plan of
     distribution not previously disclosed in the registration statement or any
     material change to such information in the registration statement;

     Provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply
if the registration statement is on Form S-3 or Form S-8 and the information
required to be included in a post-effective amendment by those paragraphs is
contained in periodic reports filed by the registrant pursuant to section 13
or section 15(d) of the Securities Exchange Act of 1934 that are incorporated
by reference in the registration statement.

     (2)  That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be deemed to
be a new registration statement relating to the securities offered therein,
and the offering of such securities at that time shall be deemed to be the
initial bona fide offering thereof.

     (3)  To remove from registration by means of a post-effective amendment
any of the securities being registered which remain unsold at the termination
of the offering.

(b)  The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act of 1934 that is incorporated by reference in the
registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such
securities at that time shall be deemed to be the initial bona fide offering
thereof.

(h)  Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to directors, officers, and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the
registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the
Act and is, therefore, unenforceable.  In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrant of expenses incurred or paid by a director, officer, or controlling

                                       4
<PAGE>
 
person of the registrant in the successful defense of any action, suit, or
proceeding) is asserted by such director, officer, or controlling person
connected with the securities being registered, the registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Act and will
be governed by the final adjudication of such issue.

                                       5
<PAGE>
 
                                  SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Minneapolis, State of Minnesota, on September 30,
1996.

                                       UROLOGIX, INC.


                                       By   /s/ Jack E. Meyer
                                         ---------------------------------------
                                         Jack E. Meyer, President and
                                         Chief Executive Officer

                               POWER OF ATTORNEY

     The undersigned officers and directors of Urologix, Inc., hereby constitute
and appoint Jack E. Meyer and Wesley E. Johnson, or either of them, with power
to act one without the other, our true and lawful attorney-in-fact and agent,
with full power of substitution and resubstitution, for us and in our stead, in
any and all capacities to sign any and all amendments (including post-effective
amendments) to this Registration Statement and all documents relating thereto,
and to file the same, with all exhibits thereto, and other documents in
connection therewith, with the Securities and Exchange Commission, granting unto
said attorney-in-fact and agent, full power and authority to do and perform each
and every act and thing necessary or advisable to be done in and about the
premises, as fully to all intents and purposes as he might or could do in
person, hereby ratifying and confirming all that said attorney-in-fact and
agent, or his substitutes, may lawfully do or cause to be done by virtue hereof.

     Pursuant to the requirements of the Securities Act of 1933, as amended,
this registration statement has been signed below on September 30, 1996 by the
following persons in the capacities indicated.

SIGNATURE                                   TITLE
---------                                   -----


/s/ Mitchell Dann                           Chairman of the Board
----------------------------------------                                   
    Mitchell Dann


/s/ Jack E. Meyer                           Director, President and Chief
----------------------------------------    Executive Officer (principal       
    Jack E. Meyer                           executive officer)
                                               

/s/ Wesley E. Johnson                       Vice President, Chief Financial
----------------------------------------    Officer and Secretary              
    Wesley E. Johnson                       (principal accounting officer) 
                                               

/s/ Buzz Benson                             Director
----------------------------------------                      
    Buzz Benson


/s/ Janet G. Effland                        Director
----------------------------------------                      
    Janet G. Effland


/s/ Michael R. Henson                       Director
----------------------------------------                  
    Michael R. Henson

                                       6
<PAGE>
 
/s/ Robert Momsen                           Director
----------------------------------------                  
    Robert Momsen


/s/ David C. Utz, M.D.                      Director
----------------------------------------                 
    David C. Utz, M.D.


/s/ Paul A. LaViolette                      Director
----------------------------------------                   
    Paul A. LaViolette

                                       7
[{"type": "S-8", "sequence": "1", "description": "FORM S-8", "secsgml_size_bytes": 14523}]
{"company-data": {"conformed-name": "UROLOGIX INC", "cik": "0000882873", "assigned-sic": "3845", "irs-number": "411697237", "state-of-incorporation": "MN", "fiscal-year-end": "0630"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-13271", "film-number": "96638347"}, "business-address": {"street1": "14405 21ST AVE N", "city": "MINNEAPOLIS", "state": "MN", "zip": "55447", "phone": "6124751400"}}
As filed with the Securities and Exchange Commission on October 1, 1996
                                                 Registration No. 333- _________
--------------------------------------------------------------------------------

                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549
                         ____________________________

                                   FORM S-8
                            REGISTRATION STATEMENT
                                     UNDER
                          THE SECURITIES ACT OF 1933

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

                MINNESOTA                                     41-1697237
      ------------------------------                        -------------------
     (State or other jurisdiction of                         (I.R.S. Employer
      incorporation or organization)                        Identification No.)

                            14405 21ST AVENUE NORTH
                            MINNEAPOLIS, MN   55447
               ------------------------------------------------
             (Address of Principal Executive Offices and zip code)
                       _________________________________

                                UROLOGIX, INC.
                       1996 EMPLOYEE STOCK PURCHASE PLAN
                           (Full title of the Plan)
                         ____________________________
                               Wesley E. Johnson
                                   Secretary
                                Urologix, Inc.
                            14405 21st Avenue North
                            Minneapolis, MN   55447
                                (612) 475-1400
 (Name, address, including zip code and telephone number of agent for service)

                                   Copy to:

                           Thomas G. Lovett IV, Esq.
                          Lindquist & Vennum P.L.L.P.
                                4200 IDS Center
                            80 South Eighth Street
                            Minneapolis, MN  55402
                                (612) 371-3211
                          ___________________________
CALCULATION OF REGISTRATION FEE
--------------------------------------------------------------------------------------------
 
                                               Proposed
                       Proposed Maximum         Maximum                          Amount of
 Title of Securities     Amount to be     Offering Price Per      Aggregate     Registration
  to be Registered        Registered             Share         Offering Price       Fee
 
--------------------------------------------------------------------------------------------
Common Stock,             
$.01 par value
  Total                   100,000 shares        15.375(1)          $1,537,500    $       466
                                                                   ==========      =========
--------------------------------------------------------------------------------------------
(1)  Estimated solely for the purpose of determining the registration fee
       pursuant to Rule 457(c) and (h) and based upon the average of the bid and
       asked prices of the Company's Common Stock on the Nasdaq System at the
       close of business on September 30, 1996.

  
                                       2
PART II

Item 3.   Incorporation of Documents by Reference.
------------------------------------------------- 

          The following documents filed with the Securities and Exchange
Commission are hereby incorporated by reference herein:
          
          (a) Form 10-K Annual Report of the Company for the fiscal year ended
June 30, 1996.
          
          (b) Form 8-A Registration Statement, as amended, filed with the
Securities and Exchange Commission and declared effective May 29, 1996 under
File No. 0-28414.

          All documents subsequently filed by the Company pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934, prior to the
filing of a post-effective amendment which indicates that all securities offered
have been sold or which deregisters all securities then remaining unsold, shall
be deemed to be incorporated by reference in this Registration Statement and to
be a part hereof from the date of filing of such documents.

Item 4.   Description of Securities.
-----------------------------------

          Not applicable.

Item 5.   Interests of Named Experts and Counsel.
------------------------------------------------ 

          Not applicable.

Item 6.   Indemnification of Directors and Officers.
--------------------------------------------------- 

          The Company's Bylaws and the statutes of the State of Minnesota
require the Company to indemnify any director, officer, employee or agent who
was or is a party to any threatened, pending or completed action, suit or
proceeding, whether civil, criminal, administrative or investigative, against
certain liabilities and expenses incurred in connection with the action, suit or
proceeding, except where such persons have not acted in good faith or did not
reasonably believe that the conduct was in the best interests of the Company.

          Insofar as indemnification for liabilities arising under the
Securities Act of 1933, as amended (the "Securities Act"), may be permitted to
directors, officers or other persons controlling the Company pursuant to the
foregoing provisions, the Company has been informed that in the opinion of the
Securities and Exchange Commission (the "Commission"), such indemnification is
against public policy as expressed in the Securities Act and is therefore
unenforceable.

Item 7.   Exemption from Registration Claimed.
--------------------------------------------- 

          Not Applicable.

                                       3
Item 8.  Exhibits.
----------------- 

     4.1    Urologix, Inc. 1996 Employee Stock Purchase Plan
     5.1    Opinion and Consent of Lindquist & Vennum P.L.L.P.
     23.1   Consent of Lindquist & Vennum (included in Exhibit 5)
     23.2   Consent of Arthur Andersen, LLP, Certified Public Accountants
_____________________

Item 9.  Undertakings.
--------------------- 

(a)  The undersigned registrant hereby undertakes:

     (1)  To file, during any period in which offers or sales are being made, a
post-effective amendment to this registration statement:

          (i)   To include any prospectus required by Section 10(a)(3) of the
     Securities Act of 1933;

          (ii)  To reflect in the prospectus any facts or events arising after
     the effective date of the registration statement (or the most recent post-
     effective amendment thereof) which, individually or in the aggregate,
     represent a fundamental change in the information set forth in the
     registration statement. Notwithstanding the foregoing, any increase or
     decrease in volume of securities offered (if the total dollar value of
     securities offered would not exceed that which was registered) and any
     deviation from the low or high end of the estimated maximum offering range
     may be reflected in the form of prospectus filed with the Commission
     pursuant to Rule 424(b) if, in the aggregate, the changes in volume and
     price represent no more than a 20% change in the maximum aggregate offering
     price set forth in the "Calculation of Registration Fee" table in the
     effective registration statement;

          (iii) To include any material information with respect to the plan of
     distribution not previously disclosed in the registration statement or any
     material change to such information in the registration statement;

     Provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply
if the registration statement is on Form S-3 or Form S-8 and the information
required to be included in a post-effective amendment by those paragraphs is
contained in periodic reports filed by the registrant pursuant to section 13
or section 15(d) of the Securities Exchange Act of 1934 that are incorporated
by reference in the registration statement.

     (2)  That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be deemed to
be a new registration statement relating to the securities offered therein,
and the offering of such securities at that time shall be deemed to be the
initial bona fide offering thereof.

     (3)  To remove from registration by means of a post-effective amendment
any of the securities being registered which remain unsold at the termination
of the offering.

(b)  The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act of 1934 that is incorporated by reference in the
registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such
securities at that time shall be deemed to be the initial bona fide offering
thereof.

(h)  Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to directors, officers, and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the
registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the
Act and is, therefore, unenforceable.  In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrant of expenses incurred or paid by a director, officer, or controlling

                                       4
person of the registrant in the successful defense of any action, suit, or
proceeding) is asserted by such director, officer, or controlling person
connected with the securities being registered, the registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Act and will
be governed by the final adjudication of such issue.

                                       5
SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Minneapolis, State of Minnesota, on September 30,
1996.

                                       UROLOGIX, INC.

                                       By   /s/ Jack E. Meyer
                                         ---------------------------------------
                                         Jack E. Meyer, President and
                                         Chief Executive Officer

                               POWER OF ATTORNEY

     The undersigned officers and directors of Urologix, Inc., hereby constitute
and appoint Jack E. Meyer and Wesley E. Johnson, or either of them, with power
to act one without the other, our true and lawful attorney-in-fact and agent,
with full power of substitution and resubstitution, for us and in our stead, in
any and all capacities to sign any and all amendments (including post-effective
amendments) to this Registration Statement and all documents relating thereto,
and to file the same, with all exhibits thereto, and other documents in
connection therewith, with the Securities and Exchange Commission, granting unto
said attorney-in-fact and agent, full power and authority to do and perform each
and every act and thing necessary or advisable to be done in and about the
premises, as fully to all intents and purposes as he might or could do in
person, hereby ratifying and confirming all that said attorney-in-fact and
agent, or his substitutes, may lawfully do or cause to be done by virtue hereof.

     Pursuant to the requirements of the Securities Act of 1933, as amended,
this registration statement has been signed below on September 30, 1996 by the
following persons in the capacities indicated.

SIGNATURE                                   TITLE
---------                                   -----

/s/ Mitchell Dann                           Chairman of the Board
----------------------------------------                                   
    Mitchell Dann

/s/ Jack E. Meyer                           Director, President and Chief
----------------------------------------    Executive Officer (principal       
    Jack E. Meyer                           executive officer)
                                               

/s/ Wesley E. Johnson                       Vice President, Chief Financial
----------------------------------------    Officer and Secretary              
    Wesley E. Johnson                       (principal accounting officer) 
                                               

/s/ Buzz Benson                             Director
----------------------------------------                      
    Buzz Benson

/s/ Janet G. Effland                        Director
----------------------------------------                      
    Janet G. Effland

/s/ Michael R. Henson                       Director
----------------------------------------                  
    Michael R. Henson

                                       6
/s/ Robert Momsen                           Director
----------------------------------------                  
    Robert Momsen

/s/ David C. Utz, M.D.                      Director
----------------------------------------                 
    David C. Utz, M.D.

/s/ Paul A. LaViolette                      Director
----------------------------------------                   
    Paul A. LaViolette

                                       7