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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 Form 10-K/A
  þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2010
 -OR-
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period from            to
 Commission File No. 001-33958
 RXi PHARMACEUTICALS CORPORATION
 (Exact name of registrant as specified in its charter)
 Delaware
    
    20-8099512(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification Number)60 Prescott StreetWorcester, Massachusetts
    
    01605(Address of principal executive offices)
    
    (Zip Code)
 Registrants telephone number, including area code:
(508) 767-3861
 SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:
 Title of Each Class
    
    Name of Exchange on Which RegisteredCommon Stock, $0.0001 Par Value Per Share
    
    NASDAQ Capital Market
 SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:
None
 o þ
 o þ
 þ o
 o þ
 o o
  Large accelerated filer o
    
    Accelerated filer o
    
    Non-accelerated filer o
    
    Smaller reporting company þ(Do not check if a smaller reporting company)
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TABLE OF CONTENTS
 PagePART IIIItem 10. Directors, Executive Officers and Corporate Governance.
    
    
    1Item 11. Executive Compensation.
    
    
    9Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters.
    
    
    18Item 13. Certain Relationship and Related Transactions and Director Independence.
    
    
    20Item 14. Principal Accountant Fees and Services.
    
    
    22Signatures
    
    
    24EX-31.3EX-31.4
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EXPLANATORY NOTE
   DISCLAIMER
  ii




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PART III
 
 ITEM 10.
    
    DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE.
  Name
    
    Age
    
    PositionMark J. Ahn, Ph.D.
    
    
    48
    
    
    President, Chief Executive Officer and DirectorMark W. Schwartz, Ph.D.
    
    
    56
    
    
    Executive Vice President, Chief Operating OfficerRobert E. Kennedy
    
    
    55
    
    
    Treasurer, Chief Financial OfficerRichard Chin, M.D.
    
    
    44
    
    
    DirectorStephen Galliker
    
    
    64
    
    
    DirectorSanford J. Hillsberg
    
    
    62
    
    
    Chairman of the Board of DirectorsSteven A. Kriegsman
    
    
    68
    
    
    DirectorRudolph Nisi, M.D.
    
    
    73
    
    
    DirectorAnastasia Khvorova
    
    
    41
    
    
    Chief Scientific OfficerPamela Pavco
    
    
    54
    
    
    Vice President of Pharmaceutical Development
 Mark J. Ahn, Ph.D.
 Mark W. Schwartz
 Robert E. Kennedy
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Richard Chin, M.D.
 Stephen Galliker, CPA
 Sanford J. Hillsberg, J.D.
 Steven A. Kriegsman
 2




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Rudolph Nisi, M.D.
 Anastasia Khvorova, Ph.D., (41)
 Pamela Pavco, Ph.D. (54)
 3




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ad hoc
 Nomination andCorporateClass of
    
    Audit
    
    Compensation
    
    Governance
    
    StrategyName
    
    Directors(1)
    
    Committee
    
    Committee
    
    Committee
    
    CommitteeSanford J. Hillsberg
    
    III
    
    x
    
    
    
    
    
    xMark J. Ahn, Ph.D.
    
    IIRichard Chin, M.D.
    
    III
    
    
    
    x
    
    x
    
    xStephen S. Galliker(2)
    
    II
    
    x
    
    
    
    xSteven A. Kriegsman(3)
    
    III
    
    x
    
    x
    
    
    
    xRudolph Nisi, M.D.(4)
    
    I
    
    
    
    x
    
    x
    
    x
 
 (1)
    
    Class I directors serve until the 2011 Annual Meeting of Stockholders, Class II directors serve until the 2012 Annual
Meeting of Stockholders and Class III directors serve until the 2013 Annual Meeting of Stockholders.(2)
    
    Mr. Galliker is the Chairman of the Audit Committee.(3)
    
    Mr. Kriegsman is the Chairman of the Compensation Committee and of the Strategy Committee(4)
    
    Dr. Nisi is Chairman of the Nomination and Corporate Governance Committee. Audit Committee
   
    
    The quality and integrity of our financial statements and reports.
    
    The independent registered public accounting firms qualifications and independence.
    
    The performance of our independent auditors.
  4




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www.rxipharma.com.
   Report of the Audit Committee
  
    
    appointing, overseeing and, if necessary, replacing the independent auditor.
    
    assisting our Board of Directors with oversight of the preparation of our financial
statements, our compliance with legal and regulatory requirements, the independent auditors
qualifications and independence and the performance of our independent auditor.
    
    preparing the report the SEC rules require to be included in our annual proxy statement.
    
    resolving disagreements between management and the auditor regarding financial reporting.
      5




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Respectfully submitted,Audit Committee:Stephen S. Galliker, ChairmanSanford J. HillsbergSteven A. Kriegsman
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Compensation Committee
  www.rxipharma.com.
  Nomination and Corporate Governance Committee
   
    
    identifying individuals qualified to become members of our Board of Directors.
    
    selecting, or recommending that our Board of Directors select, the director nominees for
the next annual meeting of stockholders.
    
    developing and recommending to our Board of Directors a set of applicable corporate
governance principles.
    
    overseeing and evaluating our Board of Directors and its dealings with management and
appropriate committees of the Board of Directors.
  www.rxipharma.com.
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Strategy Committee
 ad hoc
  Section 16(a) Beneficial Ownership Reporting Compliance
  Code of Ethics
 www.rxipharma.com.
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ITEM 11.
    
    EXECUTIVE COMPENSATION
 Summary Compensation Table
  Option
    
    
    All OtherSalary
    
    
    Bonus
    
    
    Awards
    
    
    Compensation
    
    
    TotalName and Principle Position
    
    Year
    
    
    ($)
    
    
    ($)(1)
    
    
    ($)(2)
    
    
    ($)(5)
    
    
    ($)Noah D. Beerman(3)
    
    
    2010
    
    
    
    376,731
    
    
    
    90,000
    
    
    
    29,455
    
    
    
    300
    
    
    
    496,486Former President and Chief Executive Officer
    
    
    2009
    
    
    
    53,365
    
    
    
    55,657
    
    
    
    690,305
    
    
    
    50
    
    
    
    799,377Amy B. Tata(4)
    
    
    2010
    
    
    
    179,954
    
    
    
    16,315
    
    
    
    61,438
    
    
    
    163
    
    
    
    257,870Former Director of Accounting
    
    
    2009
    
    
    
    112,064
    
    
    
    14,400
    
    
    
    74,274
    
    
    
    144
    
    
    
    200,882Anastasia Khvorova, Ph.D.
    
    
    2010
    
    
    
    283,752
    
    
    
    49,941
    
    
    
    198,572
    
    
    
    300
    
    
    
    532,565Chief Scientific Officer
    
    
    2009
    
    
    
    264,855
    
    
    
    42,559
    
    
    
    263,900
    
    
    
    300
    
    
    
    571,614Pamela Pavco, Ph.D.
    
    
    2010
    
    
    
    281,197
    
    
    
    38,933
    
    
    
    203,006
    
    
    
    300
    
    
    
    523,436Vice President of Pharmaceutical Development
    
    
    2009
    
    
    
    249,192
    
    
    
    36,158
    
    
    
    174,544
    
    
    
    300
    
    
    
    460,194
 
 (1)
    
    Year-end bonuses were accrued at December 31, 2010 and 2009 and paid
in January 2011 and January 2010 respectively.(2)
    
    Amounts included under Options Awards reflect the grant date fair
value computed in accordance with FASB ASC 718 for the indicated year,
adjusted to disregard the effects of any estimate of forfeitures
related to service-based vesting. The assumptions we used in valuing
options are described more fully in Managements Discussion and
Analysis and the footnotes to our financial statements incorporated
herein by reference to our annual report on Form 10-K for the year
ended December 31, 2010.(3)
    
    Mr. Beerman became President and Chief Executive Officer on November
5, 2009. He resigned effective March 31, 2011(4)
    
    Ms. Tata served as our acting principal financial officer during 2010.
She left our company effective April 13, 2011.(5)
    
    Consists of life insurance premiums paid by us. RXi Pharmaceuticals Corporations 2007 Incentive Plan
  9




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Outstanding Equity Awards
  Option AwardsNumber of
    
    
    Number ofSecurities
    
    
    SecuritiesUnderlying
    
    
    UnderlyingUnexercised
    
    
    Unexercised
    
    
    OptionOptions
    
    
    Options
    
    
    Exercise
    
    
    OptionExercisable
    
    
    Unexercisable
    
    
    Price
    
    
    ExpirationName
    
    (#)
    
    
    (#)
    
    
    ($)
    
    
    DateNoah D. Beerman(1)
    
    
    87,500
    
    
    
    262,500
    
    
    
    2.19
    
    
    
    11/5/2019President and Chief Executive Officer
    
    
    1,086
    
    
    
    4,706
    
    
    
    5.66
    
    
    
    1/14/2020Amy B. Tata(2)
    
    
    16,250
    
    
    
    3,750
    
    
    
    5.00
    
    
    
    8/16/2017Director of Accounting
    
    
    8,340
    
    
    
    5,013
    
    
    
    7.50
    
    
    
    4/18/20188,750
    
    
    
    11,250
    
    
    
    4.19
    
    
    
    1/15/20192,265
    
    
    
    9,816
    
    
    
    5.66
    
    
    
    1/14/2020Anastasia Khvorova, Ph.D.(3)
    
    
    95,000
    
    
    
    95,000
    
    
    
    10.43
    
    
    
    10/17/2018Chief Scientific Officer
    
    
    31,250
    
    
    
    68,750
    
    
    
    2.92
    
    
    
    9/22/20195,096
    
    
    
    22,086
    
    
    
    5.66
    
    
    
    1/14/20201,875
    
    
    
    13,125
    
    
    
    4.41
    
    
    
    4/15/2020Pamela Pavco, Ph.D.(4)
    
    
    136,229
    
    
    
    9,082
    
    
    
    5.00
    
    
    
    5/23/2017Vice President of Pharmaceutical Development
    
    
    26,140
    
    
    
    15,686
    
    
    
    7.50
    
    
    
    4/18/201820,562
    
    
    
    26,438
    
    
    
    4.19
    
    
    
    1/15/20195,260
    
    
    
    22,794
    
    
    
    5.66
    
    
    
    1/14/20201,875
    
    
    
    13,125
    
    
    
    4.41
    
    
    
    4/15/2020
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(1)
    
    The stock option grant to Mr. Beerman with an exercise price equal to $2.19
vests in 16 equal monthly installments beginning on February 5, 2010. The stock
option grant with an exercise price of $5.66 vests in 16 equal monthly
installments beginning on April 14, 2010. Mr. Beerman resigned on March 31,
2011, and there will be no further vesting of his options after that date.(2)
    
    The stock option grant to Ms. Tata with an exercise price equal to $5.00
vests in 16 equal quarterly installments beginning on November 16, 2007. The
stock option grant with an exercise price equal to $7.50 vests in 16 equal
quarterly installments of beginning on July 18, 2008. The stock option grant
with an exercise price equal to $4.19 vests in 16 equal quarterly installments
beginning on April 15, 2009. The stock option grant with an exercise price
equal to $5.66 vests in 16 equal installments beginning on April 14, 2010. The
stock option grant with an exercise price equal to $4.41 vests in 16 equal
installments beginning on July 15, 2010. Ms. Tata left our company effective
April 13, 2011, and there will be no further vesting of her options after that
date.(3)
    
    The stock option grant to Dr. Khvorova with an exercise price equal to
$10.43 vests in 16 equal quarterly installments beginning on January 17, 2009.
The stock option grant with an exercise price equal to $2.92 vests in 16 equal
installments beginning on December 22, 2009. The stock option grant with an
exercise price equal to $5.66 vests in 16 equal installments beginning on April
14, 2010. The stock option grant with an exercise price equal to $4.41 vests in
16 equal installments beginning on July 15, 2010. In each case, vesting is
subject to Dr. Khvorova remaining in our employ through the vesting date.(4)
    
    The stock option grant to Dr. Pavco with an exercise price equal to $5.00
vests in 16 equal quarterly installments beginning on June 7, 2007. The stock
option grant with an exercise price equal to $7.50 vests in 16 equal quarterly
installments of beginning on July 18, 2008. The stock option grant with an
exercise price equal to $4.19 vests in 16 equal quarterly installments
beginning on April 15, 2009. The stock option grant with an exercise price
equal to $5.66 vests in 16 equal installments beginning on April 14, 2010. The
stock option grant with an exercise price equal to $4.41 vests in 16 equal
installments beginning on July 15, 2010. In each case, vesting is subject to
Dr. Pavco remaining in our employ through the vesting date. Pension Benefits
  Nonqualified Defined Compensation
  Termination-Based Compensation
  Termination Agreements
 Noah D. Beerman
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Amy B. Tata
    Anastasia Khvorova, Ph.D.
   Pamela Pavco, Ph.D.
  12




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Employment Agreements
 Mark J. Ahn, Ph.D.
  13




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Mark W. Schwartz, Ph. D.
   Robert E. Kennedy
  14




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Pamela Pavco, Ph.D.
  Anastasia Khvorova, Ph.D.
  15




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Director Compensation
   Fees Earnedor Paid
    
    
    Stock
    
    
    
    
    
    
    All OtherName
    
    in Cash ($)
    
    
    Awards ($)
    
    
    Option Awards ($)(1)
    
    
    Compensation ($)
    
    
    Total ($)Mark. J. Ahn, Ph.D.(2)
    
    
    64,500
    
    
    
    
    
    
    
    245,875
    
    
    
    
    
    
    
    310,375Richard Chin, M.D.
    
    
    49,000
    
    
    
    
    
    
    
    245,875
    
    
    
    
    
    
    
    294,875Stephen S. Galliker
    
    
    73,500
    
    
    
    
    
    
    
    245,875
    
    
    
    
    
    
    
    319,375Sanford J. Hillsberg
    
    
    103,000
    
    
    
    
    
    
    
    245,875
    
    
    
    
    
    
    
    348,875Steven A. Kriegsman
    
    
    65,750
    
    
    
    
    
    
    
    463,520
    
    
    
    
    
    
    
    529,270Rudolph Nisi, M.D.
    
    
    55,000
    
    
    
    
    
    
    
    245,875
    
    
    
    
    
    
    
    300,875
 
 (1)
    
    Amounts included under options awards reflect the grant date fair value computed in
accordance with ASC 718 for the indicated year, adjusted to disregard the effects of
any estimate of forfeitures related to service-based vesting. The assumptions we
used in valuing options are described more fully in Managements Discussion and
Analysis of Financial Condition and Results of Operations and the footnotes to our
financial statements contained in this Annual Report on Form 10-K.(2)
    
    Dr. Ahn was appointed as our President and Chief Executive Officer on March 31, 2011. Cash Compensation
  
    
    an annual retainer fee of $20,000 for each director, payable quarterly,
    
    an annual retainer fee of $10,000 for the chairperson of each committee of our Board of
Directors other than the audit committee, payable quarterly,
    
    an annual retainer fee of $20,000 for the chairperson of the audit committee of our Board
of Directors, payable quarterly,
    
    an annual retainer fee of $40,000 for the Chairman of our Board of Directors, payable
quarterly,
    
    a fee of $1,500 per board meeting attended by the director, such fee payable for meetings
attended in person or telephonically,
    
    a fee of $1,500 per audit committee meeting attended by the chair of the committee, such
fees payable for meetings attended in person or telephonically,
    
    a fee of $1,250 per audit committee meeting attended by other directors who are members
of the committee, such fees payable for meetings attended in person or telephonically,
    
    a fee of $1,250 per all other committee meetings attended by the chair of the committee,
such fees payable for meetings attended in person or telephonically,
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
    
    a fee of $1,000 per all other committee meeting attended by other directors who are
members of the committee, such fees payable for meetings attended in person or
telephonically, and
 Equity Compensation
     ad hoc
  Reimbursements
  Tax and Accounting Implications
 Deductibility of Executive Compensation
  17




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Accounting for Share-Based Compensation
  Risk Assessment of Compensation Policies and Practices
  Board Leadership Structure and Role in Risk Oversight
    Compensation Committee Interlocks and Insider Participation in Compensation Decisions
  
 ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER
MATTERS
 Securities Authorized for Issuance Under Equity Compensation Plans
 Number of
    
    
    
    
    
    
    Number of SecuritiesSecurities to be
    
    
    
    
    
    
    Remaining AvailableIssued upon
    
    
    Weighted-Average
    
    
    for Future IssuanceExercise of
    
    
    Exercise of
    
    
    Under CompensationOutstanding
    
    
    Outstanding
    
    
    Plans (ExcludingOptions,
    
    
    Options, Warrants
    
    
    Securities RelatedPlan Category
    
    Warrants and Rights
    
    
    and Rights
    
    
    in (a))Equity compensation plans approved by security holders:2007 Incentive Plan
    
    
    4,333,136
    
    
    $
    5.10
    
    
    
    2,199,497Equity compensation plans not approved by security holders
    
    
    
    
    
    
    
    
    
    
    Total
    
    
    4,333,136
    
    
    $
    5.10
    
    
    
    2,199,497
 18




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Beneficial Ownership of RXis Common Stock
  
    
    any person known by us to be the beneficial owner of 5% or more of our common stock,
including any group as that term is defined in the Exchange Act;
    
    each current director and our named executive officers; and
    
    all of our current directors and executive officers as a group.
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Amount and Nature
    
    
    Percentage ofof Beneficial
    
    
    OutstandingName of Beneficial Owner
    
    Ownership
    
    
    SharesMark J. Ahn, Ph.D.(1)
    
    
    312,500
    
    
    
    *Mark W. Schwartz, Ph.D.
    
    
    337,661
    
    
    
    *Robert E. Kennedy(2)
    
    
    379,298
    
    
    
    *Anastasia Khvorova(3)
    
    
    219,053
    
    
    
    *Pamela Pavco, Ph.D.(4)
    
    
    255,572
    
    
    
    *Richard Chin, M.D.(5)
    
    
    112,500
    
    
    
    *Stephen S. Galliker(6)
    
    
    222,500
    
    
    
    *Sanford J. Hillsberg(7)
    
    
    439,339
    
    
    
    1.0
    %Steven A. Kriegsman(8)
    
    
    467,500
    
    
    
    1.1
    %Rudolph Nisi, M.D.(9)
    
    
    216,000
    
    
    
    *All executive officers and directors as a group  9 persons (10)
    
    
    2,961,923
    
    
    
    7.1
    %
 
 *
    
    Represents less than 1%.(1)
    
    Consists of shares of common stock underlying stock options.(2)
    
    Represents shares acquired in our recent acquisition of Apthera. Approximately 10% of the shares shown are currently
held in an escrow agreement among RXi, Computershare Trust Company, N.C., and Mr. Kennedy, in his capacity as the
representative of the former Apthera stockholders. The escrow share are subject to release from escrow in two equal
installments on or about October 13, 2011 and April 13, 2012, respectively. In the meantime, the beneficial owner retains
voting power with respect to the escrow shares. Of the shares shown, 2,432 shares are owned of record by Mr. Kennedys wife
and 2,577 shares are owned of record by Ringneck Investments, a private limited liability company of which Mr. Kennedy is
the managing member and, as such, has voting and investment power with respect to such shares. Mr. Kennedy disclaims
beneficial ownership of the shares held by Ringneck Investments in excess of his 5.66% equity interest in Ringneck
Investments.(3)
    
    Includes 168,494 shares of common stock underlying stock options.(4)
    
    Includes 215,632 shares of common stock underlying stock options.(5)
    
    Consists of shares of common stock underlying stock options.(6)
    
    Includes 212,500 shares of common stock underlying stock
options.(7)
    
    Includes 312,500 shares of common stock underlying stock
options.(8)
    
    Includes 462,500 shares of common stock underlying stock options.(9)
    
    Includes 212,500 shares of common stock underlying stock options.(10)
    
    Includes 2,009,124 shares of common stock underlying stock options. 
 ITEM 13. CERTAIN RELATIONSHIP, RELATED TRANSACTIONS AND DIRECTOR INDEPENDENCE
 Transactions with Related Persons
 General
  Policies and Procedures for Related Person Transactions
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
    
    that all related person transactions, all material terms of the transactions, and all the
material facts as to the related persons direct or indirect interest in, or relationship
to, the related person transaction must be communicated to the Audit Committee; and
    
    that all related person transactions, and any material amendment or modification to any
related person transaction, be reviewed and approved or ratified by the Audit Committee, as
required by NASDAQ Marketplace Rules.Our Audit Committee will evaluate related person transactions based on:
    
    Information provided by members of our Board of Directors in connection with the required
annual evaluation of director independence;
    
    Pertinent responses to the Directors and Officers Questionnaires submitted periodically
by our officers and directors and provided to the Audit Committee by our management;
    
    Background information on nominees for director provided by the Nominating and Corporate
Governance Committee of our Board of Directors; and
    
    Any other relevant information provided by any of our directors or officers.
    Acquisition of Apthera
    21




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Director Independence
    
 ITEM 14.
    
    PRINCIPAL ACCOUNTANT FEES AND SERVICES
 Audit Fees
  Audit Related Fees
  Tax Fees
  22




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All Other Fees
  Pre-Approval Policies and Procedures
  23




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SIGNATURES
  RXi PHARMACEUTICALS CORPORATIONDated: May 2, 2011
    By:
    /s/  Mark J. AhnMark J. Ahn, Ph.D.President and Chief Executive Officer  Signatures
    
    Title
    
    Date/s/ Mark J. Ahn
    
    President, Chief Executive Officer and Director
    
    May 2, 2011Mark J. Ahn, Ph.D.
    
    (Principal Executive Officer)/s/ Robert E. Kennedy
    
    Vice President and Chief Financial Officer
    
    May 2, 2011Robert E. Kennedy
    
    (Principal
Financial Officer)/s/ Sanford J. Hillsberg
    
    Director
    
    May 2, 2011Sanford J. Hillsberg/s/ Richard Chin
    
    Director
    
    May 2, 2011Richard Chin/s/ Stephen S. Galliker
    
    Director
    
    May 2, 2011Stephen S. Galliker/s/ Steven A. Kriegsman

Steven A. Kriegsman
    
    Director
    
    May 2, 2011
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ExhibitNumber
    
    Description31.3
    
    Sarbanes-Oxley Act Section 302 Certification of Mark J. Ahn31.4
    
    Sarbanes-Oxley Act Section 302 Certification of Robert E. Kennedy