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Confidential Treatment Requested

by BioCryst Pharmaceuticals, Inc.

    Brian J. Lane

    FOIA Confidential Treatment Request

    Direct: 202.887.3646

    Fax: 202.530.9589

    September 9, 2010

    BLane@gibsondunn.com

Client: C 12412-00001

VIA EDGAR

Mr. Jim Rosenberg

Division of Corporation Finance

United States Securities and Exchange Commission

100 F Street, NE

Washington, D.C. 20549

    Re:

    BioCryst Pharmaceuticals, Inc.

    Form 10-K for the year ended December 31, 2009

    Filed March 9, 2010

    Definitive Proxy Statement on Schedule 14A

    Filed April 6, 2010

    File No. 000-23186

Dear Jim:

On behalf of BioCryst Pharmaceuticals, Inc. (the “Company”) this responds to your letter of August
25, 2010 with respect to the above-referenced filings. For ease of reference, the numbered
paragraphs below correspond to the numbered comments in your letter, with your comments presented
in bold followed by the related response.

Pursuant to 17 C.F.R. § 200.83, the Company is requesting confidential treatment for portions of
the response to comment 4. The Company requests that these portions, as indicated by [***], be
maintained in confidence, not be made part of any public record and not be disclosed to any person
as they contain confidential information, disclosure of which would cause the Company competitive
harm. In the event that the Staff receives a request for access to the confidential portions
herein, whether pursuant to the Freedom of Information Act (“FOIA”) or otherwise, the Company
respectfully requests that it be notified immediately so that it may further substantiate this
request for confidential treatment. Please address any notification of a request for access to such
documents to the office of the General Counsel at the Company.

Form 10-K for the year ended December 31, 2009

Management’s Discussion and Analysis of Financial Condition and Results of Operations
2009 Corporate Highlights

Peramivir, page 40

    Mr. Jim Rosenberg

    Confidential Treatment Requested

    September 9, 2010

    by BioCryst Pharmaceuticals, Inc.

    Page 2

    1.

    Refer to your disclosure that “We have determined that there is an excess of up to $5.0
million of peramivir active pharmaceutical ingredient (“API”) manufactured under the contract
with HHS. This excess API is beyond the amount necessary to support U.S. regulatory
approval...We are evaluating whether additional quantities of peramivir API are needed by the
Company, and if so, the acquisition process to obtain the API from HHS.” Please provide us
proposed disclosure to include in your September 30, 2010 Form 10-Q that provides a chronology
and description of events leading up to and subsequent to your determination of the excess.
Also include in the proposed disclosure the effects and expected effects of the excess on your
results of operations and financial position, and clarify why you are evaluating whether
additional quantities are needed if there is an excess. Finally, include in the proposed
disclosure how you have accounted for the excess in your financial statements.

     In its Annual Report on Form 10-K for the year ended December 31, 2009, the Company described
its contract with the Department of Health and Human Services (“HHS”) as follows: In
January 2007, the Company was awarded a contract from HHS for the advanced development of its
influenza neuraminidase inhibitor, peramivir, for the treatment of seasonal and life-threatening
influenza. The contract was awarded at an amount of $102.6 million to support manufacturing,
process validation, clinical studies, and other development activities for peramivir. In
September 2009, the contract was modified to award the Company an additional $77.2 million in order
to perform Phase 3 studies and other development activities for intravenous peramivir. The
Company’s advanced development contract with HHS is a cost-plus-fixed-fee contract. That is, the
Company is entitled to receive reimbursement for all costs incurred in accordance with the contract
provisions that are related to the development of peramivir plus a fixed fee, or profit.

     To address the Staff’s question regarding the issue of excess API manufactured under the
contract with HHS, the Company plans to provide the following disclosure in its Quarterly Report on
Form 10-Q for the quarterly period ended September 30, 2010:

     “Under the defined scope of work in the contract with HHS for the development of peramivir, a
process was undertaken to validate a U.S.-based manufacturer and the related method for producing
commercial batches of peramivir active pharmaceutical ingredient (“API”). As a required outcome of
this validation process, large quantities of peramivir API were produced. In accordance with its
accounting practices, the Company recorded all costs associated with this validation process as R&D
expenses in its Statements of Operations. Simultaneously, revenue from the HHS contract was also
recorded in the Company’s Statement of Operations. HHS subsequently reimbursed the Company for
these costs and upon reimbursement from HHS, the associated peramivir API became property of the
U.S. government.

    Mr. Jim Rosenberg

    Confidential Treatment Requested

    September 9, 2010

    by BioCryst Pharmaceuticals, Inc.

    Page 3

     Under the terms of the contract, if the Company determines the amount of API produced under
the contract is in excess of what is necessary to complete the contract, the Company can acquire
any excess peramivir API at cost to use for its own purposes. The Company believes that as a
result of the manufacturing campaign described above, more peramivir API has been produced than is
required to support U.S. regulatory approval. Therefore, the Company determined that there was an
excess of up to $5.0 million of peramivir API manufactured under this validation process. HHS is
reviewing the Company’s estimate calculation, but has acknowledged that at least half of the amount
in the Company’s estimate is indeed excess to the requirements of the HHS contract. The Company is
evaluating whether any of the excess peramivir API will be needed by the Company to support other
contracts, partners, or activities, and if so, the acquisition process to obtain the excess API
from HHS. Acquisition of a portion or all of the excess peramivir API from HHS will impact the
Company’s financial statements.”

Schedule 14A filed April 6, 2010

    2.

    We note that you have not included any disclosure in response to Item 402(s) of Regulation
S-K. Please advise us of the basis for your conclusion that disclosure is not necessary and
describe the process you undertook to reach that conclusion.

     During the Company’s proxy preparation process in the first quarter of 2010, management of the
Company, together with the Company’s compensation consultant and outside counsel and Compensation
Committee, examined the Company’s compensation program and discussed whether any elements of the
program created risks that were reasonably likely to have a material adverse effect on the Company.
Following this analysis, management concluded that the elements of the Company’s compensation
program did not create risks that are reasonably likely to have a material adverse effect on the
Company, and therefore that disclosure under Item 402(s) was not required.

     In its analysis, management considered a number of factors, including primarily: (1) the total
value of the payments made under the Company’s compensation program for the prior year and (2) that
any corporate actions that would potentially lead to achievement of individual or corporate
performance objectives would require approval by the Company’s Board of Directors, which provides a
check on the ability of any individual to take risks that could have a material adverse effect on
the Company in an effort to achieve a certain performance objective.

    Mr. Jim Rosenberg

    Confidential Treatment Requested

    September 9, 2010

    by BioCryst Pharmaceuticals, Inc.

    Page 4

Corporate Governance

Board Leadership Structure, page 18

    3.

    We note that the company has chosen to separate the principal executive officer and board
chairman positions. Please confirm that in future filings, you will expand your disclosure to
discuss why the company believes that this board leadership structure is the most appropriate
structure for the company at the time of filing. Please refer to Item 407(h) of Regulation
S-K.

     The Company confirms that in applicable future filings it will explicitly state why the
Company has determined that the leadership structure of the Board is the most appropriate in light
of the circumstances that exist at that time.

Compensation Discussion and Analysis

Annual Incentive Compensation, page 24

    4.

    You disclose on page 24 that overall funding for annual incentive compensation is based on
your performance against the current year corporate objectives. On page 25, you state that
the Committee approved an AIP pool equal to 93% of the target incentive amount. Please
provide us proposed disclosure to be included in an amendment to your Form 10-K for the year
ended December 31, 2009 to identify the corporate objectives used by the Committee to
determine the potential size of the pool allocated for annual incentive compensation. In
addition, please discuss how the level of achievement of each corporate objective corresponded
to the Committee’s determination that the AIP pool would be equal to 93% of the target
incentive amount.

     The Company omitted disclosure of the corporate objectives used by the Compensation Committee
to determine the potential size of the pool allocated for annual incentive compensation because it
believes that, based on established case law standards, such objectives constitute confidential
commercial information, the disclosure of which would cause competitive harm, and that therefore
such objectives would be entitled to confidential treatment. Instruction 4 to Item 402(b) of
Regulation S-K provides that registrants are not required to disclose any factors or criteria
involving confidential commercial information, the disclosure of which would result in competitive
harm for the registrant.

    Mr. Jim Rosenberg

    Confidential Treatment Requested

    September 9, 2010

    by BioCryst Pharmaceuticals, Inc.

    Page 5

     [*** Redacted***]

     The Company will provide additional disclosure in its applicable future filings with respect
to the overall nature of the corporate objectives, including more specific examples that would
increase the understanding of the objectives without providing competitively sensitive information.
The Company will also provide additional disclosure in applicable future filings about the process
used by the Compensation Committee to determine the size of the pool for annual incentive
compensation.

     As an illustration, the Company would propose to disclose the following with respect to the
corporate objectives in its 2011 Proxy Statement:

     “The corporate objectives established for 2010 were primarily related to the continued
progression of both our clinical and non-clinical programs. The corporate objectives fell into
three primary categories: (1) clinical development objectives, which constituted a substantial
majority of the 2010 corporate objectives and consisted of specific, detailed goals with respect to
the advancement of the Company’s clinical programs; (2) licensing and financing objectives, which
related to potential partnering, licensing and other alliance relationships related to the
Company’s current product candidates and the development of new product candidates, as well as
management of the Company’s cash position and expenses; and (3) early stage project objectives,
which related to the development of various specific early-stage product candidates.”

    5.

    We note that the NEOs achieved 2009 bonus payments based on the achievement of corporate
objectives and individual objectives. Your Compensation Discussion and Analysis does not
disclose the corporate nor individual objectives used to determine these executive officers’
annual performance-based bonus. Please provide us proposed disclosure to be included in an
amendment to your Form 10-K for the year ended December 31, 2009 to provide the following:

    •

    The corporate and individual performance objectives;

    •

    The portion of the bonus attributable to the achievement of corporate objectives
and individual objectives; and

    •

    A discussion of how the level of achievement of each objective affected the actual
bonuses to be paid.

     To the extent that the objectives are quantitative, the discussion should also be
quantitative. Please also disclose the level of achievement of these objectives.

    Mr. Jim Rosenberg

    Confidential Treatment Requested

    September 9, 2010

    by BioCryst Pharmaceuticals, Inc.

    Page 6

     As discussed in the response to comment 4 with respect to corporate objectives, the Company
omitted disclosure of the corporate objectives used by the Committee because it believes that,
based on established case law standards, such objectives constitute confidential commercial
information, the disclosure of which would cause competitive harm, and that therefore such
objectives would be entitled to confidential treatment. The Company disclosed in the Proxy
Statement that the individual objectives were prepared in conjunction with the corporate objectives
and were designed to promote the execution of the corporate objectives. Because the individual
objectives are of a similar nature as the corporate objectives, the Company believes that the
individual objectives constitute confidential commercial information and that disclosure of the
individual objectives would cause the Company competitive harm, for the same reasons detailed in
the response to comment 4. It therefore believes that disclosure of the individual objectives
would result in substantial competitive harm to the Company and that they are therefore not
required to be disclosed.

     The Company will provide additional disclosure in its applicable future filings with respect
to the overall nature of the corporate and individual objectives, including more specific examples
that would increase the understanding of the objectives without providing competitively sensitive
information.

     With respect to the portion of the bonus attributable to the achievement of corporate and
individual objectives for 2009, the Company disclosed in the Proxy Statement that the corporate
objectives are used to determine the overall funding for the AIP pool, and that the allocation of
the pool is determined based on the achievement of the individual objectives. The Company will
clarify in applicable future filings the way the corporate objectives and individual objectives
work together to result in a final bonus determination. For 2009, the corporate objectives
essentially acted as a multiplier applied to the achievement of the individual objectives (as an
example, if an executive achieved 95% of individual objectives, and the corporate objectives were
achieved at 50%, the executive would receive 45% of the target incentive amount). The disclosure
of both the amounts awarded under the AIP in 2009 in the Proxy Statement, and the AIP pool equal to
93% of target provided all of the information needed to determine the achievement of each
individual’s objectives.

     As an illustration, the Company would propose to disclose the following with respect to the
individual objectives (assuming the named executive officers for 2010 will be the same as those for
2009) and the interaction between the individual objectives and the corporate objectives in its
2011 Proxy Statement:

     “The individual objectives established for the named exe