UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549





FORM 10-Q







|x | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ---------------------------------------------------------------------------------------

FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2008

or



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transaction period from  to

Commission File Number 0-28414





UROLOGIX, INC.

(Exact name of registrant as specified in its charter)







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

14405 21st Avenue North, Minneapolis, MN 55447

(Address of principal executive offices)

Registrants telephone number, including area code: (763) 475-1400





Indicate by check mark whether the registrant
(1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and
(2) has been subject to such filing requirements for the past 90 days.    Yes  x    No   ̈

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See definition
of accelerated filer and large accelerated filer in Rule 12b-2 of the Exchange Act.



|                        |  |   |  |                           |  |  
|----------------------- |  | - |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈ |  | Accelerated filer         |  |  ̈
|                        |  |   | 
|Non-accelerated filer   |  |  ̈ |  | Smaller reporting company |  | x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange
Act).    Yes   ̈    No  x

As of November 1, 2008, the Company had outstanding 14,463,350 shares of common stock, $.01 par value.









---

PART I  FINANCIAL INFORMATION



|ITEM 1. | FINANCIAL STATEMENTS
|------- | --------------------

Urologix, Inc.

Condensed Balance Sheets

(In thousands, except per share data)



|                                                                                             |  |                   |          |   |              |   |         |  
|-------------------------------------------------------------------------------------------- |  | ----------------- | -------- | - | ------------ | - | ------- | -
|                                                                                             |  | September 30,2008 |          |   | June 30,2008 |  
|                                                                                             |  | (unaudited)       |          |   | (*)          |  
|ASSETS                                                                                       |  |                   |          |   |              |   |         |  
|Current assets:                                                                              |  |                   |          |   |              |   |         |  
|Cash and cash equivalents                                                                    |  | $                 | 9,197    |   |              | $ | 11,031  |  
|Accounts receivable, net of allowances of $98 and $153, respectively                         |  |                   | 1,401    |   |              |   | 1,773   |  
|Inventories                                                                                  |  |                   | 1,627    |   |              |   | 1,634   |  
|Prepaids and other current assets                                                            |  |                   | 291      |   |              |   | 115     |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Total current assets                                                                         |  |                   | 12,516   |   |              |   | 14,553  |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Property and equipment:                                                                      |  |                   |          |   |              |   |         |  
|Machinery, equipment and furniture                                                           |  |                   | 12,258   |   |              |   | 12,303  |  
|Less accumulated depreciation                                                                |  |                   | (10,416  | ) |              |   | (10,295 | )
|                                                                                             |  |                   |          |   |              |   |         |  
|Property and equipment, net                                                                  |  |                   | 1,842    |   |              |   | 2,008   |  
|Other assets                                                                                 |  |                   | 714      |   |              |   | 752     |  
|Other intangible assets, net                                                                 |  |                   | 161      |   |              |   | 167     |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Total assets                                                                                 |  | $                 | 15,233   |   |              | $ | 17,480  |  
|                                                                                             |  |                   |          |   |              |   |         |  
|                                                                                             |  |                  
|LIABILITIES AND SHAREHOLDERS EQUITY                                                         |  |                   |          |   |              |   |         |  
|Current liabilities:                                                                         |  |                   |          |   |              |   |         |  
|Accounts payable                                                                             |  | $                 | 594      |   |              | $ | 774     |  
|Accrued compensation                                                                         |  |                   | 351      |   |              |   | 711     |  
|Deferred income                                                                              |  |                   | 257      |   |              |   | 227     |  
|Other accrued expenses                                                                       |  |                   | 1,048    |   |              |   | 1,582   |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Total current liabilities                                                                    |  |                   | 2,250    |   |              |   | 3,294   |  
|Deferred income                                                                              |  |                   | 293      |   |              |   | 339     |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Total liabilities                                                                            |  |                   | 2,543    |   |              |   | 3,633   |  
|                                                                                             |  |                   |          |   |              |   |         |  
|COMMITMENTS AND CONTINGENCIES (Note 10)                                                      |  |                   |          |   |              |   |         |  
|Shareholders equity:                                                                        |  |                   |          |   |              |   |         |  
|Common stock, $.01 par value, 25,000 shares authorized; 14,383 shares issued and outstanding |  |                   | 144      |   |              |   | 144     |  
|Additional paid-in capital                                                                   |  |                   | 113,530  |   |              |   | 113,413 |  
|Accumulated deficit                                                                          |  |                   | (100,984 | ) |              |   | (99,710 | )
|                                                                                             |  |                   |          |   |              |   |         |  
|Total shareholders equity                                                                   |  |                   | 12,690   |   |              |   | 13,847  |  
|                                                                                             |  |                   |          |   |              |   |         |  
|Total liabilities and shareholders equity                                                   |  | $                 | 15,233   |   |              | $ | 17,480  |  
|                                                                                             |  |                   |          |   |              |   |         |  



|(*) | The Balance Sheet at June 30, 2008 has been derived from the audited financial statements at that date but does not include all of the information and footnotes required by
generally accepted accounting principles for complete financial statements.
|--- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

The accompanying notes to financial statements
are an integral part of these statements.



2



---

Urologix, Inc.

Condensed Statements of Operations

(In thousands, except per share data)

(Unaudited)



|                                                                         |  |                                 |        |   |      |   |        |  
|------------------------------------------------------------------------ |  | ------------------------------- | ------ | - | ---- | - | ------ | -
|                                                                         |  | Three Months EndedSeptember 30, |       
|                                                                         |  | 2008                            |        |   | 2007 |  
|Sales                                                                    |  | $                               | 2,655  |   |      | $ | 4,351  |  
|Cost of goods sold                                                       |  |                                 | 1,484  |   |      |   | 1,629  |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Gross profit                                                             |  |                                 | 1,171  |   |      |   | 2,722  |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Costs and expenses:                                                      |  |                                 |        |   |      |   |        |  
|Selling, general and administrative                                      |  |                                 | 1,829  |   |      |   | 2,501  |  
|Research and development                                                 |  |                                 | 622    |   |      |   | 678    |  
|Amortization of identifiable intangible assets                           |  |                                 | 6      |   |      |   | 9      |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Total costs and expenses                                                 |  |                                 | 2,457  |   |      |   | 3,188  |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Operating loss                                                           |  |                                 | (1,286 | ) |      |   | (466   | )
|Interest income, net                                                     |  |                                 | 46     |   |      |   | 143    |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Loss before taxes                                                        |  |                                 | (1,240 | ) |      |   | (323   | )
|Provision for income tax expense                                         |  |                                 | 34     |   |      |   | 74     |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Net loss                                                                 |  | $                               | (1,274 | ) |      | $ | (397   | )
|                                                                         |  |                                 |        |   |      |   |        |  
|Net loss per common sharebasic                                          |  | $                               | (0.09  | ) |      | $ | (0.03  | )
|                                                                         |  |                                 |        |   |      |   |        |  
|Net loss per common sharediluted                                        |  | $                               | (0.09  | ) |      | $ | (0.03  | )
|                                                                         |  |                                 |        |   |      |   |        |  
|Weighted average number of shares used in basic per share calculations   |  |                                 | 14,383 |   |      |   | 14,333 |  
|                                                                         |  |                                 |        |   |      |   |        |  
|Weighted average number of shares used in diluted per share calculations |  |                                 | 14,383 |   |      |   | 14,333 |  
|                                                                         |  |                                 |        |   |      |   |        |  

The accompanying notes to financial statements are an integral part of these statements.



3



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Urologix, Inc.

Condensed Statements of Cash Flows

(In thousands)

(Unaudited)



|                                                                                          |  |                                 |        |   |      |   |        |  
|----------------------------------------------------------------------------------------- |  | ------------------------------- | ------ | - | ---- | - | ------ | -
|                                                                                          |  | Three Months EndedSeptember 30, |       
|                                                                                          |  | 2008                            |        |   | 2007 |  
|Operating Activities:                                                                     |  |                                 |        |   |      |   |        |  
|Net loss                                                                                  |  | $                               | (1,274 | ) |      | $ | (397   | )
|Adjustments to reconcile net loss to net cash provided by (used in) operating activities: |  |                                 |        |   |      |   |        |  
|Depreciation and amortization                                                             |  |                                 | 287    |   |      |   | 278    |  
|Provision for bad debts                                                                   |  |                                 | 1      |   |      |   | 7      |  
|Employee stock-based compensation expense                                                 |  |                                 | 117    |   |      |   | 225    |  
|Deferred income taxes                                                                     |  |                                 |       |   |      |   | 74     |  
|Change in operating items:                                                                |  |                                 |        |   |      |   |        |  
|Accounts receivable                                                                       |  |                                 | 371    |   |      |   | 408    |  
|Inventories                                                                               |  |                                 | (92    | ) |      |   | (4     | )
|Prepaids and other assets                                                                 |  |                                 | (138   | ) |      |   | (189   | )
|Accounts payable                                                                          |  |                                 | (180   | ) |      |   | (196   | )
|Accrued expenses and deferred income                                                      |  |                                 | (910   | ) |      |   | (414   | )
|                                                                                          |  |                                 |        |   |      |   |        |  
|Net cash used in operating activities                                                     |  |                                 | (1,818 | ) |      |   | (208   | )
|                                                                                          |  |                                 |        |   |      |   |        |  
|Investing Activities:                                                                     |  |                                 |        |   |      |   |        |  
|Purchase of property and equipment                                                        |  |                                 | (16    | ) |      |   | (62    | )
|                                                                                          |  |                                 |        |   |      |   |        |  
|Net cash used in investing activities                                                     |  |                                 | (16    | ) |      |   | (62    | )
|                                                                                          |  |                                 |        |   |      |   |        |  
|Financing Activities:                                                                     |  |                                 |        |   |      |   |        |  
|Net cash provided by financing activities                                                 |  |                                 |       |   |      |   |       |  
|                                                                                          |  |                                 |        |   |      |   |        |  
|Net decrease in cash and cash equivalents                                                 |  |                                 | (1,834 | ) |      |   | (270   | )
|Cash and cash equivalents:                                                                |  |                                 |        |   |      |   |        |  
|Beginning of period                                                                       |  |                                 | 11,031 |   |      |   | 12,250 |  
|                                                                                          |  |                                 |        |   |      |   |        |  
|End of period                                                                             |  | $                               | 9,197  |   |      | $ | 11,980 |  
|                                                                                          |  |                                 |        |   |      |   |        |  
|Supplemental cash-flow information                                                        |  |                                 |        |   |      |   |        |  
|Net carrying amount of inventory transferred to property and equipment                    |  | $                               | 99     |   |      | $ | 129    |  

The accompanying notes to financial statements are an integral part of these statements.



4



---

Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



|1. | Basis of Presentation
|-- | ---------------------

The accompanying unaudited
condensed financial statements of Urologix, Inc. (the Company, Urologix, we) have been prepared in accordance with generally accepted accounting principles for interim financial information and with the
instructions for Form 10-Q and Article 10 of Regulation S-X. The balance sheet as of September 30, 2008 and the statements of operations and cash flows for the three-month periods ended September 30, 2008 and 2007 are unaudited but include
all adjustments (consisting of normal recurring adjustments) necessary for a fair presentation of the financial position at such date and the operating results and cash flows for those periods. Certain information normally included in financial
statements and related footnotes prepared in accordance with generally accepted accounting principles has been condensed or omitted pursuant to the rules and regulations of the Securities and Exchange Commission. The accompanying financial
statements should be read in conjunction with the financial statements and notes included in the Urologix Annual Report on Form 10-K for the year ended June 30, 2008.

Results for any interim period shown in this report are not necessarily indicative of results to be expected for any other interim period or for the
entire year.



|2. | Significant Accounting Policies
|-- | -------------------------------

Revenue Recognition

We recognize revenue from the sale of Cooled ThermoTherapy system control units upon delivery to the customer. In addition to our
sales of Cooled ThermoTherapy system control units, we place our Cooled ThermoTherapy system control units with customers under a variety of programs for both evaluation and long-term use, and also provide access to Cooled ThermoTherapy treatments
via our Cooled ThermoTherapy mobile service. We retain title to the control units placed with our customers for evaluation and longer-term use and do not recognize any revenue on these control units until title has transferred. These programs, as
well as our Cooled ThermoTherapy mobile service, are designed to expand access to our technology, and thus expand the market for our single-use treatment catheters. Revenue from our mobile service is recognized upon treatment of the patient. Revenue
from the sale of single-use treatment catheters is recognized at the time of shipment. Revenue for warranty service contracts is deferred and recognized over the contract period and revenue subject to certain sales incentives is deferred based upon
the contract provisions. We record a provision for estimated sales returns on product sales in the same period as the related revenue is recorded. The provision for estimated sales returns is based on historical sales returns, analysis of credit
memo data and specific customer-based circumstances. Sales and use taxes are reported on a net basis, excluding them from revenue.



|3. | Use of Estimates
|-- | ----------------

The preparation of financial
statements in conformity with U.S. generally accepted accounting principles requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the
date of the financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.



5



---

Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



|4. | Stock-Based Compensation
|-- | ------------------------

We have a stock option plan that provides for the granting of incentive stock options to employees and nonqualified stock options and restricted stock to employees, directors and consultants. As of September 30,
2008, we had reserved 4,450,910 shares of common stock under this plan, and 1,009,613 shares were available for future grants. Options expire ten years from the date of grant and typically vest 25 percent after the first year of service with the
remaining vesting 1/36theach month thereafter. Under the current terms of our stock option plan, persons serving as non-employee directors at the
date of the annual shareholder meeting automatically receive a grant to purchase 10,000 shares of common stock at a price equal to fair market value on the date of grant. Generally, such options are immediately exercisable on the date of grant, and
expire 10 years from the date of grant, subject to earlier termination one year after the person ceases to be a director of the Company.

On July 1, 2005, we adopted the fair value recognition provisions of Statement of Financial Accounting Standards (SFAS) No. 123R Share-Based Payment using the modified prospective method. As a result, our results of
operations for the three month periods ended September 30, 2008 and 2007 reflect compensation expense recognized over the requisite service period for new stock options granted since July 1, 2005, and the unvested portion of stock option
grants made prior to July 1, 2005 which vested during those periods. Amounts recognized in the financial statements related to stock-based compensation were as follows (in thousands):



|                                           |  |                                 |     |      |   |    
|------------------------------------------ |  | ------------------------------- | --- | ---- | - | ---
|                                           |  | Three months endedSeptember 30,
|                                           |  | 2008                            |     | 2007
|Cost of goods sold                         |  | $                               | 7   |      | $ | 32 
|Selling, general and administrative        |  |                                 | 99  |      |   | 167
|Research and development                   |  |                                 | 11  |      |   | 26 
|                                           |  |                                 |     |      |   |    
|Total cost of stock-based compensation     |  | $                               | 117 |      | $ | 225
|Tax benefit of options issued              |  |                                 |    |      |   |   
|                                           |  |                                 |     |      |   |    
|Total stock-based compensation, net of tax |  | $                               | 117 |      | $ | 225
|                                           |  |                                 |     |      |   |    

The fair value of each option grant is estimated on the date of grant using the Black-Scholes
option-pricing model. We use historical data to estimate expected volatility, the period of time that option grants are expected to be outstanding, as well as employee termination behavior. The risk-free rate is based on the U.S. Treasury yield
curve in effect at the time of grant for the estimated life of the option. The following assumptions were used to estimate the fair value of options granted during the three-month periods ended September 30, 2008 and 2007 using the
Black-Scholes option-pricing model:



|                        |  |           |   |  |           |  
|----------------------- |  | --------- | - |  | --------- | -
|                        |  | 2008      |   |  | 2007      |  
|Volatility              |  | 55.4      | % |  | 62.7      | %
|Risk-free interest rate |  | 2.7       | % |  | 4.7       | %
|Expected option life    |  | 3.0 years |   |  | 3.1 years |  
|Stock dividend yield    |  |          |   |  |          |  



6



---

Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



A summary of our option activity for the three-month period ended September 30, 2008 is as
follows:



|                                  |  |                  |   |  |                                       |      |                                        |     |                          |   |        
|--------------------------------- |  | ---------------- | - |  | ------------------------------------- | ---- | -------------------------------------- | --- | ------------------------ | - | -------
|                                  |  | Number ofOptions |   |  | Weighted-avg.Exercise Price PerOption |      | Weighted-avg.RemainingContractual Term |     | Aggregate IntrinsicValue
|Outstanding at July 1, 2008       |  | 1,614,450        |   |  | $                                     | 3.32 |                                        |     |                          | $ | 107,013
|Options granted                   |  | 253,000          |   |  |                                       | 1.84 |                                        |     |                          |   |        
|Options forfeited                 |  | (138,106         | ) |  |                                       | 2.06 |                                        |     |                          |   |        
|Options expired                   |  | (75,277          | ) |  |                                       | 6.00 |                                        |     |                          |   |        
|Options exercised                 |  |                 |   |  |                                       |     |                                        |     |                          |   |        
|                                  |  |                  |   |  |                                       |      |                                        |     |                          |   |        
|Outstanding at September 30, 2008 |  | 1,654,067        |   |  |                                       | 3.08 |                                        | 7.4 |                          | $ | 27,773 
|Exercisable at September 30, 2008 |  | 901,072          |   |  |                                       | 4.09 |                                        | 5.5 |                          | $ | 16,125 

The aggregate intrinsic value in the table above is based on our closing stock price of $1.79 and $1.21 as of the
last business day of July 1, 2008 and September 30, 2008, respectively, which would have been received by the optionees had all in-the-money options been exercised on such dates.

A summary of restricted stock award activity for the three-month period ended September 30, 2008 is as follows:



|                                |  |                                 |  |                                   |     
|------------------------------- |  | ------------------------------- |  | --------------------------------- | ----
|                                |  | Number ofRestricted StockAwards |  | Weighted-avg.Grant-Date FairValue
|Nonvested at July 1, 2008       |  | 80,000                          |  | $                                 | 1.79
|Options granted                 |  |                                |  |                                   |    
|Options forfeited               |  |                                |  |                                   |    
|Options vested                  |  |                                |  |                                   |    
|                                |  |                                 |  |                                   |     
|Nonvested at September 30, 2008 |  | 80,000                          |  | $                                 | 1.79
|                                |  |                                 |  |                                   |     

As of September 30, 2008, total unrecognized compensation cost related to nonvested stock
options and restricted stock awards granted under our plan was $828,000 and $93,000 respectively. That cost is expected to be recognized over a weighted-average period of 2.7 years for non-vested stock options and 3.7 years for restricted stock
awards.



|5. | Basic and Diluted Loss Per Share
|-- | --------------------------------

Basic loss per
share is computed by dividing the net loss by the weighted average number of shares of common stock outstanding during the periods presented. Diluted loss per share is computed by dividing the net loss by the weighted average number of shares of
common stock outstanding plus all dilutive potential common shares that result from stock options. The weighted average common shares outstanding for both basic and dilutive, were 14,383 and 14,333 at September 30, 2008 and 2007, respectively.



7



---

Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



The dilutive effect of stock options excludes approximately 1,599,786 and 1,271,000 shares for the
three-month periods ended September 30, 2008 and 2007, respectively of options for which the exercise price was higher than the average market price. In addition, 31,528 and zero of potentially dilutive stock options where the exercise price
was lower than the average market price were excluded from diluted weighted average common shares outstanding for the three-month periods ended September 30, 2008 and 2007 respectively, as they would be anti-dilutive due to our net loss for
such periods.



|6. | Inventories
|-- | -----------

Inventories consisted of the following as of (in
thousands):



|                  |  |                   |       |              |   |      
|----------------- |  | ----------------- | ----- | ------------ | - | -----
|                  |  | September 30,2008 |       | June 30,2008
|Raw materials     |  | $                 | 814   |              | $ | 786  
|Work in process   |  |                   | 279   |              |   | 264  
|Finished goods    |  |                   | 534   |              |   | 584  
|                  |  |                   |       |              |   |      
|Total inventories |  | $                 | 1,627 |              | $ | 1,634
|                  |  |                   |       |              |   |      



|7. | Other Accrued Expenses
|-- | ----------------------

Other accrued expenses were
comprised of the following as of (in thousands):



|                             |  |                   |       |              |   |      
|---------------------------- |  | ----------------- | ----- | ------------ | - | -----
|                             |  | September 30,2008 |       | June 30,2008
|Accrued severance            |  | $                 | 366   |              | $ | 405  
|Sales tax accrual            |  |                   | 365   |              |   | 762  
|Other                        |  |                   | 317   |              |   | 415  
|                             |  |                   |       |              |   |      
|Total other accrued expenses |  | $                 | 1,048 |              | $ | 1,582
|                             |  |                   |       |              |   |      

Based on a recent sales tax audit and new information obtained by the Company in the fourth
quarter of fiscal 2008, we believed we may have additional sales tax exposure in some states related to our mobile service business. As a result, we felt a liability was probable under Statement of Financial Accounting Standard (SFAS) No. 5
Accounting for Contingencies and increased our sales tax accrual by approximately $755,000 in the fourth quarter of fiscal 2008 for sales we believed to be exempt. As a result of new information obtained subsequent to June 30, 2008,
which indicates that we will not owe as much sales tax as previously estimated, we reduced our sales tax accrual by approximately $396,000 to $365,000 at September 30, 2008, resulting in a reduction in our selling, general and administrative
expenses for the three-month period ended September 30, 2008.



8



---

Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



|8. | Income Taxes
|-- | ------------

The Company adopted the provisions of
FASB Interpretation No. 48, Accounting for Uncertainty in Income Taxes, an Interpretation of FASB Statement No. 109 (FIN 48) on July 1, 2007. This interpretation clarifies the accounting for uncertainty in income taxes
recognized in an entitys financial statements in accordance with SFAS 109, Accounting for Income Taxes. It prescribes a recognition threshold and measurement attribute for financial statement disclosure of tax positions taken or
expected to be taken on a tax return. As of June 30, 2008, the liability for gross unrecognized tax benefits was an immaterial amount. During the three months ended September 30, 2008, there were no significant changes to the total gross
unrecognized tax benefits. It is expected that the amount of unrecognized tax benefits for positions which we have identified will not change significantly in the next twelve months.

We file income tax returns in the United States (U.S.) federal jurisdiction as well as various state jurisdictions. We are subject to U.S. federal income
tax examinations by tax authorities for fiscal years after 1993. Income tax examinations we may be subject to for the various state taxing authorities vary by jurisdiction.



|9. | Warranty
|-- | --------

Our products are covered by warranties
against defects in material and workmanship for periods of up to 24 months. We record a liability for warranty claims at the time of sale. The amount of the liability is based on the trend in the historical ratio of product failure rates, material
usage and service delivery costs to sales, the historical length of time between the sale and resulting warranty claim, and other factors.

Warranty provisions and claims for the three-month periods ended September 30, 2008 and 2007 were as follows (in thousands):



|            |  |                            |     |                                |   |     |                |  |   |                               |   |  |   |   
|----------- |  | -------------------------- | --- | ------------------------------ | - | --- | -------------- |  | - | ----------------------------- | - |  | - | --
|Fiscal Year |  | BeginningBalanceat July 1, |     | WarrantyProvisions(Reductions) |   |     | WarrantyClaims |  |   | EndingBalanceat September 30,
|2009        |  | $                          | 40  |                                | $ | 1   |                |  | $ | (13                           | ) |  | $ | 28
|2008        |  | $                          | 105 |                                | $ | (44 | )              |  | $ | (16                           | ) |  | $ | 45



|10. | Commitments and Contingencies
|--- | -----------------------------

Legal Proceedings

We have been and are involved in various legal proceedings and other matters that arise in the normal course of our business, including
product liability claims that are inherent in the testing, production, marketing and sale of medical devices. The ultimate liabilities, if any, cannot be determined at this time. However, based upon currently available information, we believe that
the ultimate resolution of these matters will not have a material effect on the financial position, liquidity or results of operations of the Company.



|11. | Recently Issued Accounting Pronouncements
|--- | -----------------------------------------

In
September 2006, the FASB issued Statement of Financial Accounting Standard (SFAS) No. 157, Fair Value Measurements. SFAS No. 157 establishes a single authoritative definition of fair value, sets out a framework



9



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Urologix, Inc.

Notes to Condensed Financial Statements

September 30, 2008

(Unaudited)



for measuring fair value and requires additional disclosures about fair-value measurements. This Statement applies only to fair value measurements that are
already required or permitted by other accounting standards, except for measurements of share-based payments and measurements that are similar to, but not intended to be, fair value. This statement is expected to increase the consistency of fair
value measurements, but imposes no requirements for additional fair value measures in financial statements. The provisions under SFAS No. 157 were effective for us beginning on July 1, 2008. The adoption of this statement had no impact on
our financial statements.

In February 2007, the FASB issued SFAS No.159, The Fair Value Option for Financial Assets and Financial
Liabilities. SFAS No. 159 amends SFAS No. 115, Accounting for Certain Investments in Debt and Equity Securities and permits entities to choose to measure many financial instruments and certain other items at fair value.
SFAS No. 159 was effective for us beginning on July 1, 2008. The adoption of this statement had no impact on our financial statements.

In December 2007, the FASB issued Statement of Financial Accounting Standards No. 141(R) (revised 2007), Business Combinations (SFAS 141R). SFAS 141(R) establishes principles and requirements for how an
acquirer recognizes and measures in its financial statements the identifiable assets acquired, the liabilities assumed, any noncontrolling interest in the acquiree and the goodwill acquired in the business combination. SFAS 141(R) also
establishes disclosure requirements to enable the evaluation of the nature and financial effects of the business combination. SFAS 141(R) will impact financial statements at the acquisition date and in subsequent periods. We will be required to
apply the new guidance to any business combinations completed on or after July 1, 2009.

In April 2008, the FASB issued FASB Staff
Position (FSP) No. 142-3, Determination of the Useful Life of Intangible Assets. FSP No. 142-3 amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a
recognized intangible asset under SFAS No. 142, Goodwill and Other Intangible Assets. FSP No. 142-3 is effective for us beginning July 1, 2009. We do not expect the adoption of this statement to have any impact on our
financial statements.

In October 2008, the FASB issued FSP no. FAS 157-3, Determining the Fair Value of a Financial Asset When the
Market for That Asset is Not Active which clarifies the application of SFAS 157 in an inactive market and illustrates how an entity would determine fair value when the market for a financial asset is not active. The Staff Position is effective
immediately and applies to prior periods for which financial statements have not been issued, including interim or annual periods ending on or before September 28, 2008. The implementation of FAS 157-3 had no impact on our financial statements.



10



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|ITEM 2. | MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS
|------- | -------------------------------------------------------------------------------------

This Managements Discussion and Analysis of Financial Condition and Results of Operations contains, in addition to historical information,
forward-looking statements that are based on our current expectations, beliefs, intentions or future strategies. These statements are subject to risks and uncertainties that could cause actual results to differ materially from the statements as a
result of certain factors, including those set forth under Part I, Item 1A. Risk Factors in our Annual Report on Form 10-K for the year ended June 30, 2008, as well as in other filings we make with the Securities and Exchange
Commission and include factors such as: the impact of competitive treatments, products and pricing; our ability to develop and market new products and services, including the Urologix-owned Cooled ThermoTherapy mobile service and the
CoolWave control unit and our ability to generate revenue from new products such as CTC Advance; our dependence upon third-party reimbursement for our products and reimbursement rates for Cooled ThermoTherapy; our dependence on Cooled
ThermoTherapy for all of our revenues; approval by the FDA of our products, and compliance with FDA requirements for the manufacture, labeling, marketing and sale of our products; the rate of adoption by the medical community of Cooled ThermoTherapy
products and the effectiveness of our sales organization and marketing efforts to the medical and patient community; our limited experience in manufacturing some of our products and our dependence upon third-party suppliers to produce and supply
products; our ability to successfully defend our intellectual property against infringement and the expense associated with that effort; product liability claims inherent in the testing, production, marketing and sale of medical devices; product
recalls which could harm our reputation and business; and our ability to obtain additional financing if needed on reasonable terms. All forward-looking statements included herein are based on information available to us as of the date hereof, and we
undertake no obligation to update any such forward-looking statements.

The following is a discussion and analysis of Urologix
financial condition and results of operations as of and for the three-month periods ended September 30, 2008 and 2007. This section should be read in conjunction with the condensed financial statements and related notes in Item 1 of this
report and Urologix Annual Report on Form 10-K for the year ended June 30, 2008.

OVERVIEW

Urologix develops, manufactures, and markets non-surgical, catheter-based therapies that use a
proprietary cooled microwave technology for the treatment of benign prostatic hyperplasia (BPH), a disease that affects more than 23 million men worldwide. We market our control units under the Targis® and CoolWave® names and our procedure kits under the recently approved CTC Advance, CTC, Targis and Prostaprobe names. All systems utilize
the Companys Cooled ThermoTherapy technology, a targeted microwave energy combined with a unique cooling mechanism that protects healthy tissue and enhances patient comfort while providing safe, effective, lasting relief from the
symptoms of BPH. Cooled ThermoTherapy can be performed without general anesthesia or intravenous sedation and can be performed in a physicians office or an outpatient clinic. We believe that Cooled ThermoTherapy provides an efficacious, safe
and cost-effective solution for BPH with results clinically superior to medication and without the complications and side effects inherent in surgical procedures.

We believe that third-party reimbursement is essential to the continued adoption of Cooled ThermoTherapy, and that clinical efficacy, overall cost-effectiveness and physician advocacy will be keys to maintaining such
reimbursement. We estimate that 60% to 80% of patients who receive Cooled ThermoTherapy treatment in the United States will be eligible for Medicare coverage. The remaining patients will either be covered by private insurers, including traditional
indemnity health insurers and managed care organizations, or they will be private-paying patients. As a result, Medicare reimbursement is particularly critical for widespread market adoption of Cooled ThermoTherapy in the United States.

The level of Medicare reimbursement for Cooled ThermoTherapy is dependent on the site of service. Beginning on August 1, 2000, the Centers for
Medicare and Medicaid Services (CMS) replaced the reasonable cost



11



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basis of reimbursement for outpatient hospital-based procedures, including Cooled ThermoTherapy, with a new fixed rate or prospective payment system. Under
this method of reimbursement, a hospital receives a fixed reimbursement for each Cooled ThermoTherapy treatment performed in its outpatient facility, $3,026 in calendar year 2009 compared to $2,879 in calendar year 2008, although the rate varies
depending on a wage index and other factors for each region. The urologist performing the Cooled ThermoTherapy treatment receives reimbursement of approximately $587 per procedure.

In January 2001, CMS began to reimburse for Cooled ThermoTherapy treatments performed in the urologists office. The reimbursement rate (inclusive
of the physicians fee) in calendar year 2009 for Cooled ThermoTherapy procedures performed in the urologists office is $2,551 compared to $3,118 in calendar 2008, which is subject to geographic adjustment.

In January 2008, the CPT Code covering Cooled ThermoTherapy was once again added to the Ambulatory Surgical Centers (ASC) list of Medicare approved
procedures. Effective with this change, urologists who perform Cooled ThermoTherapy procedures in an ASC are reimbursed under the two-part system in which the ASC receives a fixed fee of $1,849 for calendar year 2009, as compared to $1,872 in
calendar 2008, while the urologist performing the treatment is reimbursed approximately $587 for calendar year 2009.

We have an active
reimbursement strategy, and have retained consultative experts to assist us with reimbursement matters, including the reimbursement rate reductions for calendar year 2009.

Private insurance companies and HMOs make their own determinations regarding coverage and reimbursement based upon usual and customary fees.
To date, we have received coverage and reimbursement in various geographies from private insurance companies and HMOs throughout the United States. We intend to continue our efforts to gain coverage and reimbursement across the United States. There
can be no assurance that we will receive favorable coverage or reimbursement determinations for Cooled ThermoTherapy from these payers or that amounts reimbursed to physicians for performing Cooled ThermoTherapy procedures will be sufficient to
encourage physicians to use Cooled ThermoTherapy.

Our goal is to grow Cooled ThermoTherapy as a standard of care for the treatment of BPH.
Our business strategy to achieve this goal is to (i) educate both patients and physicians on the benefits of Cooled ThermoTherapy compared to other treatment options, (ii) increase the use of Cooled ThermoTherapy by physicians who already
have access to a Cooled ThermoTherapy system, (iii) increase the number of physicians who provide Cooled ThermoTherapy to their patients, and (iv) provide more physicians with access to Cooled ThermoTherapy through the use of third party
mobile providers and our own Cooled ThermoTherapy mobile service in the United States.

We expect to continue to invest in research and
development and clinical trials, sales and marketing programs and our Cooled ThermoTherapy mobile service as we focus on growing revenues and continuing to improve our therapy. Our future growth will be dependent upon, among other factors, our
success in achieving increased treatment volume and market adoption of the Cooled ThermoTherapy procedures in the physicians office, including treatments delivered through our Cooled ThermoTherapy mobile service, our success in obtaining and
maintaining necessary regulatory clearances, as well as the risk of FDA mandated recall of our products, our ability to manufacture at the volumes and quantities the market requires, the fact that our products may be subject to product recalls even
after receiving FDA clearance or approval, the extent to which Medicare and other health care payers continue to reimburse costs of Cooled ThermoTherapy procedures performed in physicians offices, hospitals, and ambulatory surgery centers and
the amount of reimbursement provided.

Critical Accounting Policies:

A description of our critical accounting policies was provided in the Managements Discussion and Analysis of Financial Condition and Results of Operations section of our Annual Report on Form 10-K for the
year ended June 30, 2008. At September 30, 2008, our critical accounting policies and estimates continue to include revenue recognition, allowance for doubtful accounts, product warranty, inventories, sales tax accrual, income taxes, and
stock-based compensation.



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RESULTS OF OPERATIONS

Net Sales

Net sales for the three-month period ended September 30, 2008 were $2.7 million compared to $4.4
million during the same period of the prior fiscal year. The $1.7 million or 39 percent decrease in net sales in the three-month period ended September 30, 2008 is primarily attributable to reduced orders from our direct office accounts and
third-party mobiles, as well as a reduction in the number of treatments performed by our Urologix-owned Cooled ThermoTherapy mobile service. The reduction in orders for direct accounts and third-party mobiles is a result of a reduction in the number
of accounts ordering and a reduction in the size of orders. The decrease in procedures performed by our Urologix mobile is due to a decrease in treatment volume of some accounts, lost accounts, transferring some accounts to third-party mobiles and
disruption in some of the mobile routes.

During the first quarter of fiscal 2009, 32 percent of sales were derived from treatment catheter
sales to direct accounts, compared to 47 percent in the prior fiscal year, while third party mobile revenue represented 14 percent of overall revenue compared to 13 percent in the prior fiscal year. Revenue derived from the Urologix-owned Cooled
ThermoTherapy mobile service constituted 50 percent of overall revenue in the current quarter compared to 40 percent of revenues in the first quarter of fiscal 2008.

Cost of Goods Sold and Asset Impairments and Gross Profit

Cost of goods sold includes raw
materials, labor, overhead, and royalties incurred in connection with the production of our Cooled ThermoTherapy system control units and single-use treatment catheters, amortization related to developed technologies, as well as costs associated
with the delivery of our Cooled ThermoTherapy mobile service. Cost of goods sold for the three-month period ended September 30, 2008 decreased by $145,000 or nine percent to $1.5 million from $1.6 million during the three-month period ended
September 30, 2007. The decrease in costs of goods sold is a result of lower sales partially offset by under absorbed manufacturing expenses of approximately $210,000.

Gross profit as a percentage of sales for the three-month period ended September 30, 2008 decreased to 44 percent from 63 percent in the three-month
period ended September 30, 2007. The 19 percentage point decrease in gross margin is primarily due to higher manufacturing and overhead rates as well as $210,000 of under absorbed manufacturing expenses mentioned above as a result of decreased
production due to the lower sales.

Selling, General & Administrative

Selling, general and administrative expenses decreased $672,000 or 27 percent to $1.8 million for the three-month period ended September 30, 2008
from $2.5 million in the same period of fiscal year 2008. The decrease in expense is primarily the result of the reversal of $396,000 of the $755,000 sales tax reserve recorded in the fourth quarter of fiscal 2008 as a result of new information
obtained subsequent to June 30, 2008, which indicates that we will not owe as much sales tax as previously estimated. In addition, sales and marketing expenses decreased by approximately $275,000 due to an $106,000 decrease in commissions as a
result of the lower sales, $100,000 decrease in stock-based compensation expense due to forfeitures and less options issued and at lower fair market values, as well as an approximate $83,000 decrease in advertising, promotions, conventions and
meetings expenses.

Research and Development

Research and development expenses, which include expenditures for product development, regulatory compliance and clinical studies, decreased $56,000 or 8 percent to $622,000 from $678,000 for the three-month period
ended September 30, 2008 compared to the same period of the prior fiscal year. The decrease in expenses resulted primarily from an approximate $140,000 decrease in product testing related to the completion of work on CTC Advance, as well as an
approximate $56,000 decrease in wages due to decreased number of personnel, as well as overall decreases in most other areas of research and development. These decreases were substantially offset by an increase of approximately $193,000 in
consulting and professional services as a result of turnover in the area.

Amortization of Identifiable Intangible Assets

Amortization of identifiable intangible assets decreased to $6,000 for the three-month period ended



13



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September 30, 2008 from $9,000 in the same period of fiscal year 2008. The decrease in amortization expense is due to the fact that during the first
quarter of fiscal 2008 we were still amortizing our trademark intangible asset and our customer base intangible asset at a higher net book value. The trademark intangible asset was subsequently written off and our customer base intangible asset
further impaired by $24,000 during the second quarter of fiscal 2008 as a result of reduced sales projections for the Prostatron product line. The current quarter amortization expense relates only to the amortization of the customer base intangible
asset over its remaining useful life of 6 years.

Net Interest Income

Net interest income for the three-month period ended September 30, 2008 decreased to $46,000 from $143,000 in the same period of the prior fiscal
year. The decrease is due to lower cash balances and lower interest rates.

Provision for Income Taxes

We recorded $34,000 of tax expense in the first quarter of fiscal 2009 compared to $74,000 in the first quarter of fiscal 2008. The prior year income tax
expense related to the deferred tax liability which could not be offset against definite-lived deferred tax assets resulting from the amortization of goodwill for tax purposes. The decrease in the income tax expense in the current period is due to
the subsequent reversal of the indefinite-lived deferred tax liability related to goodwill, which was no longer necessary after the impairment of goodwill at December 31, 2007. Our tax expense in the current year period primarily relates to
state taxes. At September 30, 2008, we continued to carry a full valuation allowance of $40.9 million against our net deferred tax assets.

LIQUIDITY AND CAPITAL RESOURCES

We have financed our operations since inception through sales of equity securities and
sales of our Cooled ThermoTherapy system control units, single-use treatment catheters and mobile service offerings. As of September 30, 2008, we had total cash and cash equivalents of $9.2 million compared to $11.0 million as of June 30,
2008. Working capital decreased to $10.3 million at September 30, 2008 from $11.3 million at June 30, 2008. The decrease in working capital is primarily due to the $1.8 million decrease in the cash balance, partially offset by the $1.0
million decrease in other current liabilities.

During the three months ended September 30, 2008, we used $1.8 million of cash for
operating activities compared to $208,000 for the three months ended September 30, 2007. The decrease in the net operating cash flows of $1.6 million is largely due to the year-to-date net loss of $1.3 million, as well as the decrease in
accrued expenses. The net loss of $1.3 million included non-cash charges of $287,000 of depreciation and amortization expense, and $117,000 of stock-based compensation expense. Changes in operating items resulted in the use of $949,000 of operating
cash flow for the period with lower accrued expense and deferred income of $910,000, accounts payable of $180,000, and prepaid and other assets increasing by $138,000, partially offset by a decrease in accounts receivable of $371,000. The decrease
in accrued expenses and deferred income resulted mainly from the reduction in the sales tax accrual, the payment of severance accruals and the payment of fiscal 2008 year end sales commissions during fiscal 2009 which were based primarily on higher
sales volumes in the month ended June 30, 2008 compared to the month ended September 30, 2008. The decrease in accounts payable is due to the timing of purchases versus payments. The increase in prepaids and other current assets is largely
due to the prepayment of insurance premiums for fiscal 2009 at the beginning of the first quarter. The decrease in accounts receivable is due to decreased sales.

During the three months ended September 30, 2008, we used $16,000 for investing activities to purchase property and equipment to support our operations.

During the three months ended September 30, 2008, no cash was generated by or used for financing activities.

We plan to continue offering customers a variety of programs for both evaluation and longer-term use of our Cooled ThermoTherapy system control units in
addition to purchase options, as well as grow our mobile service



14



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which provides physicians and patients with efficient access to our Cooled ThermoTherapy system control units on a pre-scheduled basis. As of
September 30, 2008, our property and equipment, net, included approximately $1.3 million of control units used in evaluation or longer-term use programs and units used in our Company-owned mobile service. Depending on the growth of these
programs, we may use additional capital to finance these programs.

We believe our $9.2 million in cash and cash equivalents at
September 30, 2008 will be sufficient to fund our working capital and capital resources needs for fiscal 2009. In addition, we believe our cash equivalents are secure as substantially all are backed by United States Government Treasuries. There
can be no assurance, however, that we will not require additional financing in the future or that any additional financing will be available to us on satisfactory terms, if at all.

Off Balance Sheet Arrangements

We do not have any off balance sheet arrangements.

Recently Issued Accounting Standards

In September
2006, the FASB issued Statement of Financial Accounting Standard (SFAS) No. 157, Fair Value Measurements. SFAS No. 157 establishes a single authoritative definition of fair value, sets out a framework for measuring fair value
and requires additional disclosures about fair-value measurements. This Statement applies only to fair value measurements that are already required or permitted by other accounting standards, except for measurements of share-based payments and
measurements that are similar to, but not intended to be, fair value. This statement is expected to increase the consistency of fair value measurements, but imposes no requirements for additional fair value measures in financial statements. The
provisions under SFAS No. 157 were effective for us beginning on July 1, 2008. The adoption of this statement had no impact on our financial statements.

In February 2007, the FASB issued SFAS No.159, The Fair Value Option for Financial Assets and Financial Liabilities. SFAS No. 159 amends SFAS No. 115, Accounting for Certain Investments in
Debt and Equity Securities and permits entities to choose to measure many financial instruments and certain other items at fair value. SFAS No. 159 was effective for us beginning on July 1, 2008. The adoption of this statement had no
impact on our financial statements.

In December 2007, the FASB issued Statement of Financial Accounting Standards No. 141(R) (revised
2007), Business Combinations (SFAS 141R). SFAS 141(R) establishes principles and requirements for how an acquirer recognizes and measures in its financial statements the identifiable assets acquired, the liabilities
assumed, any noncontrolling interest in the acquiree and the goodwill acquired in the business combination. SFAS 141(R) also establishes disclosure requirements to enable the evaluation of the nature and financial effects of the business
combination. SFAS 141(R) will impact financial statements at the acquisition date and in subsequent periods. We will be required to apply the new guidance to any business combinations completed on or after July 1, 2009.

In April 2008, the FASB issued FASB Staff Position (FSP) No. 142-3, Determination of the Useful Life of Intangible Assets. FSP
No. 142-3 amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset under SFAS No. 142, Goodwill and Other Intangible Assets.
FSP No. 142-3 is effective for us beginning July 1, 2009. We do not expect the adoption of this statement to have any impact on our financial statements.

In October 2008, the FASB issued FSP no. FAS 157-3, Determining the Fair Value of a Financial Asset When the Market for That Asset is Not Active which clarifies the application of SFAS 157 in an inactive
market and illustrates how an entity would determine fair value when the market for a financial asset is not active. The Staff Position is effective immediately and applies to prior periods for which financial statements have not been issued,
including interim or annual periods ending on or before September 28, 2008. The implementation of FAS 157-3 had no impact on our financial statements.



15



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|ITEM 3. | QUALITATIVE AND QUANTITATIVE DISCLOSURE ABOUT MARKET RISK
|------- | ---------------------------------------------------------

Our financial instruments include cash and cash equivalents. Increases and decreases in prevailing interest rates generally translate into decreases and increases, respectively, in the fair value of these instruments. Also, fair values of
interest rate sensitive instruments may be affected by the credit worthiness of the issuer, prepayment options, relative values of alternative instruments, the liquidity of the instrument and other general market conditions.

Market risk was estimated as the potential decrease in fair value resulting from a hypothetical 1% change in interest rates and was not materially
different from the quarter-end carrying amount. Due to the nature of our cash and cash equivalents, we have concluded that we do not have a material market risk exposure.

Our policy is not to enter into derivative financial instruments. We do not have any significant foreign currency exposure since we do not generally transact business in foreign currencies. Therefore, we do not have
significant overall currency exposure. In addition, we do not enter into any futures or forward commodity contracts since we do not have significant market risk exposure with respect to commodity prices.



|ITEM 4. | CONTROLS AND PROCEDURES
|------- | -----------------------

(a) Evaluation of Disclosure Controls
and Procedures

The Companys Chief Executive Officer, Stryker Warren, Jr., and Controller and Director of Finance, Rebecca J.
Weber, have evaluated the Companys disclosure controls and procedures as of the end of the period covered by this report. Based upon this review, they have concluded that these controls and procedures are effective.

(b) Changes in Internal Control Over Financial Reporting

There have been no changes in internal control over financial reporting that occurred during the fiscal period covered by this report that have materially affected, or are reasonably likely to materially affect, the Companys internal
control over financial reporting.

PART II - OTHER INFORMATION



|ITEM 1. | LEGAL PROCEEDINGS
|------- | -----------------

We have been and are involved in
various legal proceedings and other matters that arise in the normal course of our business, including product liability claims that are inherent in the testing, production, marketing and sale of medical devices. Based upon currently available
information, we believe that the ultimate resolution of these matters will not have a material effect on our financial position, liquidity or results of operations.



|ITEM 1A. | RISK FACTORS
|-------- | ------------

The most significant risk factors
applicable to the Company are described in Part I, Item 1A Risk Factors of our Annual Report on Form 10-K for the year ended June 30, 2008. There have been no material changes from the risk factors previously disclosed in our
Annual Report on Form 10-K.



|ITEM 2. | UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS
|------- | -----------------------------------------------------------

Not
applicable.



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|ITEM 3. | DEFAULTS UPON SENIOR SECURITIES
|------- | -------------------------------

Not applicable.



|ITEM 4. | SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS
|------- | ---------------------------------------------------

Not
applicable.



|ITEM 5. | OTHER INFORMATION
|------- | -----------------

Not applicable.



|ITEM 6. | EXHIBITS
|------- | --------



|             |  |                                                                                                               
|------------ |  | --------------------------------------------------------------------------------------------------------------
|Exhibit 31.1 |  | Certification of Chief Executive Officer Pursuant to Section 13a-14 and 15d-14 of the Exchange Act.           
|             | 
|Exhibit 31.2 |  | Certification of Controller and Director of Finance Pursuant to Section 13a-14 and 15d-14 of the Exchange Act.
|             | 
|Exhibit 32   |  | Certification pursuant to 18 U.S.C. 1350.                                                                     



17



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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.



Urologix, Inc.(Registrant)/s/ Stryker Warren, Jr.Stryker Warren, Jr.Chief Executive Officer(Principal Executive Officer)/s/ Rebecca J. WeberRebecca J. WeberController and Director of Finance(Principal Financial and Accounting Officer)Date November 14, 2008




18