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Correspondence

    ATTORNEYS AT LAW

    Broomfield, CO

    720 566-4000

    4401 Eastgate Mall

    Palo Alto, CA

    San Diego, CA

    650 843-5000

    92121-1909

    Main     858 550-6000

    Reston, VA

    Fax       858 550-6420

    703 456-8000

    July 19, 2005

    www.cooley.com

    San Francisco, CA

    415 693-2000

    JULIE M. ROBINSON

    Via Edgar and Federal Express

    (858) 550-6092

    jrobinson@cooley.com

Division of Corporation Finance

Securities and Exchange Commission

100 First Street, N.E., Mail Stop 6010

Washington, D.C. 20549

Attention: Jim B. Rosenberg, Senior Assistant Chief Accountant

                  Keira Ino, Staff Accountant

    Re:

    Gen-Probe Incorporated

Form 10-K for the Fiscal Year Ended December 31, 2004

Filed March 15, 2005
File No. 001-31279

Dear Mr. Rosenberg:

This letter is being filed on
behalf of Gen-Probe Incorporated (the “Company”) in response to
comments received from the staff of the Division of Corporation Finance of the Securities and
Exchange Commission (the “Staff”) by letter dated July 5, 2005 with respect to the above-referenced
Form 10-K (the “10-K”). The numbering of the paragraphs below corresponds to the numbering of your
comment letter, the text of which we have incorporated into this response letter for convenience.

Form 10-K for the Fiscal Year Ended December 31, 2004

General

    1.

    Comment: We note that Exhibit 10.53 to your 10-K for the fiscal year ended December 31, 2003,
is a Target License Agreement between Gen-Probe Incorporated and Tosoh Corporation, effective
as of January 1, 2004. The agreement states in section 3.1(b) that Tosoh is to pay Gen-Probe
royalties for Ribosomal Licensed Products and Ribosomal Licensed Methods that are sold,
practiced or otherwise disposed of in “Asian Countries”. Section 1.2 of the agreement defines
“Asian Countries” to include, inter alia, North Korea and Iran. In light of the fact that
North Korea and Iran have been identified by the U.S. State Department as state sponsors of
terrorism, and are subject to economic sanctions administered by the U.S. Treasury
Department’s Office of Foreign Assets Control, please advise us of the status and materiality
to you of your operations in North Korea and Iran, and give us your view as to whether those
operations, individually or in the aggregate, constitute a material investment risk for your
security holders. In preparing your response please consider that evaluations of materiality
should not be based solely on quantitative factors, but should include consideration of all
factors,

Securities and Exchange Commission

July 19, 2005

Page Two

    including the potential impact of corporate activities upon a company’s reputation and share
value, that a reasonable investor would deem important in making an investment decision.

Response: The Company
respectfully advises the Staff that it does not have any operations in North Korea or Iran and does not distribute
its products to those countries. Under the License Agreement between the Company and Tosoh
Corporation (“Tosoh”), effective as of January 1, 2004 (the “License”), the Company granted Tosoh a
worldwide, royalty-bearing license to develop, manufacture and sell products that use certain of
its technologies. Technology licenses that are worldwide in scope are common in the diagnostic
industry. However, the Company advises the Staff that Tosoh did not pay any royalties to the Company pursuant to the License prior to
the first quarter of 2005. The Company received royalties from Tosoh pursuant to the License in
the amount of $507 on product sales of $101,328 for the first quarter of 2005. All product sales
were reported to have been made in Japanese yen and the Company believes that all such sales were
made in Japan. The Company does not believe there is a market for nucleic acid diagnostic tests in
North Korea or Iran and, to the best of the Company’s knowledge, Tosoh does not contemplate sales
of licensed products in the immediate future in those countries.

The Company and its licensee Tosoh do not conduct operations or make product sales in or
to North Korea or Iran. Therefore, the Company advises the Staff that
the fact that these countries are within the territory of the worldwide
license granted to Tosoh does not create a material investment risk for the Company’s security
holders in light of the fact that no sales are currently made or contemplated to these countries.

Consolidated Financial Statements, page F-1

Notes to Consolidated Financial Statements, page F-8

2. Balance Sheet Information, page F-16

Inventories, page F-16

    2.

    Comment: Please tell us the following regarding your manufacturing variances as it is our
understanding that these are normally related to a standard cost accounting system and do not
relate to financial statements prepared in accordance with GAAP:

    •

    Comment: Whether or not the inventory balances presented on the balance sheets
are net of reserves including the manufacturing variances;

Response: The Company advises
the Staff that the inventory balances presented on the balance sheets are net of reserves and
manufacturing variances.

Securities and Exchange Commission

July 19, 2005

Page Three

    •

    Comment: A quantification of the manufacturing variances that are applied to
each stage of inventories (i.e. raw materials and supplies, work in process, and
finished good);

Response: The Company advises
the Staff that inventories, net of reserves and manufacturing variances, are presented on the balance
sheets, summarized as follows (in thousands):

    Raw

    materials

    Work in

    Finished

    and supplies

    process

    goods

    Total

    December 31, 2004:

    Gross inventory

    $
    7,240

    $
    14,509

    $
    14,626

    $
    36,375

    Excess, expired, obsolete

    (1,598
    )

    (3,117
    )

    (1,864
    )

    (6,579
    )

    Manufacturing variances

    (297
    )

    (963
    )

    (1,228
    )

    (2,488
    )

    Net inventory

    $
    5,345

    $
    10,429

    $
    11,534

    $
    27,308

    December 31, 2003:

    Gross inventory

    $
    10,371

    $
    6,140

    $
    5,859

    $
    22,370

    Excess, expired, obsolete

    (4,334
    )

    (2,563
    )

    (410
    )

    (7,307
    )

    Manufacturing variances

    (163
    )

    (459
    )

    (765
    )

    (1,387
    )

    Net inventory

    $
    5,874

    $
    3,118

    $
    4,684

    $
    13,676

    •

    Comment: A complete description of your method under which you account for the
manufacturing variances and how recording them as part of your inventory reserve
complies with GAAP;

Response: The Company advises
the Staff that the Company adjusts the carrying amount of inventory at standard cost to reflect actual
costs. Manufacturing variances occur when the standard costs of the
Company's products are not equal to the
actual costs incurred. It is Company policy to ensure that manufacturing variances are capitalized
and matched with the respective inventory as it is sold to provide proper matching of revenues and
expenses. The Company’s manufacturing variances principally comprise absorption, work order
production, and purchase price variances.

    •

    Absorption variances are defined as the difference between actual labor and overhead
costs incurred versus earned (applied at standard cost) in product work orders during a
given period. If earned labor and overhead exceed actual costs incurred, a favorable
absorption variance is realized; while an unfavorable absorption variance is realized if
actual overhead and labor costs exceed the labor and overhead earned in product work
orders.

Securities and Exchange Commission

July 19, 2005

Page Four

    •

    Work order production variances typically occur when either the quantity completed in an
operation sequence differs from the average order quantity (lot size), or the actual usage
of parts differs from the standard bill of material (usage).

    •

    Purchase price variances are caused by differences between the standard costs of our raw
materials or purchased finished goods and the actual price paid for the materials.

The Company has considered the Staff’s comment relating to the disclosure of the
Company’s manufacturing variances in
Schedule II, Valuation and Qualifying Accounts. Upon further
review, the Company has concluded that these
variances do not need to be disclosed on Schedule II since they
are adjustments that the Company records to
reflect the inventory at actual costs, as required by GAAP. As a result, in future filings, the
Company advises
the Staff that it will exclude disclosure of these GAAP adjustments from Schedule II for all periods
presented.

    •

    Comment: A quantification of the reserves that relate to the manufacturing
variances each period for each of the categories presented in Schedule II (i.e.
balance, additions and deductions); and

Response: The Company is
separately providing (below) the detail of these items, as requested by the Staff; however,
please refer to the response above indicating that, in the future,
the Company will not include manufacturing
variances in Schedule II.

The Company respectfully
advises the Staff that inventory reserves and related activity, including manufacturing variances, as presented in
Schedule II, are summarized as follows (in thousands):

Securities and Exchange Commission

July 19, 2005

Page Five

    Addition

    Balance at

    Charged to

    Balance at

    Beginning of

    Cost and

    End of

    Period

    Expenses

    Deductions

    Period

    Year Ended December 31, 2004:

    Excess, expired, obsolete

    $
    (7,307
    )

    $
    (5,506
    )

    $
    6,234

    $
    (6,579
    )

    Manufacturing variances

    (1,387
    )

    (10,362
    )

    9,261

    (2,488
    )

    $
    (8 694
    )

    $
    (15,868
    )

    $
    15,495

    $
    (9,067
    )

    Year Ended December 31, 2003:

    Excess, expired, obsolete

    $
    (10,969
    )

    $
    (5,487
    )

    $
    9,149

    $
    (7,307
    )

    Manufacturing variances

    (1,136
    )

    (6,776
    )

    6,525

    (1,387
    )

    $
    (12 105
    )

    $
    (12,263
    )

    $
    15,674

    $
    (8,694
    )

    Year Ended December 31, 2002:

    Excess, expired, obsolete

    $
    (14,057
    )

    $
    (965
    )

    $
    4,053

    $
    (10,969
    )

    Manufacturing variances

    (3
    )

    (3,150
    )

    2,017

    (1,136
    )

    $
    (14,060
    )

    $
    (4,115
    )

    $
    6,070

    $
    (12,105
    )

    •

    Comment: Why presenting the variances together with your inventory reserves is
meaningful disclosure for an investor.

Response: The Company
respectfully requests that the Staff please refer to the
Company’s response to the third bullet point above indicating
that, in the future,
the Company will exclude disclosure of manufacturing variances in Schedule II.

In addition to the responses above, the Company acknowledges that:

    •

    it is responsible for the adequacy and accuracy of the disclosure in its filings
with the Commission;

    •

    staff comments or changes to disclosure in response to staff comments do not
foreclose the Commission from taking any action with respect to the filing; and

    •

    the Company may not assert staff comments as a defense in any proceeding initiated
by the Commission or any person under the federal securities law of the United States.

If you have any questions regarding this response letter, please call the undersigned at (858)
550-6092.

Securities and Exchange Commission

July 19, 2005

Page Six

Sincerely,

Cooley Godward llp

Julie. M. Robinson

    cc:

    Henry L. Nordhoff

    R. William Bowen, Esq.

    Herm Rosenman

    Donald Tartre

    Dan Kleeberg, Ernst & Young LLP

    Frederick T. Muto, Cooley Godward LLP

    Kasia M. Biernacki, Cooley Godward LLP

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