##### Table of Contents







UNITED STATES SECURITIES AND EXCHANGE COMMISSION


WASHINGTON, DC 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, 2008


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 number: 0-24274


LA JOLLA PHARMACEUTICAL COMPANY




Delaware
    
    33-0361285(State or other jurisdiction 
of incorporation or organization)
    
    (I.R.S. Employer
Identification Number)


6455 Nancy Ridge Drive, San Diego, CA 92121


(858) 452-6600




Title of each class:
    
    Name of each exchange on which registered:Common Stock, par value $0.01 per share
    
    The Nasdaq Global Market




None


o þ


o þ


þ o


o þ


o




Large accelerated filer o
    
    Accelerated filer þ
    
    Non-accelerated filer o
    
    Smaller reporting company o(Do not check if a smaller reporting company)


o þ




DOCUMENTS INCORPORATED BY REFERENCE










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Explanatory Note
    2




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TABLE OF CONTENTS  PART IIIItem 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCEItem 11. EXECUTIVE COMPENSATIONItem 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERSItem 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCEItem 14. PRINCIPAL ACCOUNTANT FEES AND SERVICESPART IVItem 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULESSIGNATURESEXHIBIT INDEXEX-31.1EX-31.2    Table of Contents  
 PART III
 
 Item 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE.
  Name
    
    Age
    
    Position(s)Craig R. Smith, M.D
    
    
    63
    
    
    Director, Chairman of the BoardDeirdre Y. Gillespie, M.D
    
    
    53
    
    
    President, Chief Executive Officer and Assistant SecretaryGail A. Sloan, CPA
    
    
    46
    
    
    Vice President of Finance and SecretaryRobert A. Fildes, Ph.D
    
    
    70
    
    
    DirectorThomas H. Adams, Ph.D
    
    
    66
    
    
    DirectorStephen M. Martin
    
    
    62
    
    
    DirectorMartin P. Sutter
    
    
    54
    
    
    DirectorJames N. Topper, M.D., Ph.D
    
    
    47
    
    
    DirectorFrank E. Young, M.D., Ph.D
    
    
    77
    
    
    Director
  Deirdre Y. Gillespie M.D.
 Craig R. Smith, M.D.
 Gail A. Sloan CPA
 3




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##### Table of Contents



Robert A. Fildes Ph.D.
 Thomas H. Adams Ph.D.
 Stephen M. Martin
 Martin P. Sutter
 4




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James N. Topper M.D. Ph.D.
 Frank E. Young M.D. Ph.D.
 Director Independence
  Committees of the Board of Directors
  5




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##### Table of Contents



Audit Committee
   Compensation Committee
  Corporate Governance and Nominating Committee
  Meetings of Non-Management Directors
 6




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Section 16(a) Beneficial Ownership Reporting Compliance
  Code of Conduct
  
 Item 11. EXECUTIVE COMPENSATION.
 Compensation Discussion and Analysis
 Overview
 Compensation Philosophy and Objectives.
  7




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Executive Compensation Components
  
    
    base salary
    
    annual performance-based cash bonus awards
    
    equity incentive compensation
    
    other compensation
    
    benefits
 Base Salary. th
  
    
    market data provided by publicly available industry surveys and/or outside
consultants to ensure competitive compensation;
    
    compensation data for companies of a similar size, market cap and clinical
development stage;
    
    individual performance of the executive for the prior year; and
    
    internal review of the executives compensation relative to other executives to
ensure internal equity.
  Annual Performance-Based Cash Bonus Awards.
 8




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Equity Compensation .
     9




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##### Table of Contents



Other
Compensation.
 Benefits.
     Employment and Separation Agreements.
  Deirdre Y. Gillespie, M.D.
 10




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##### Table of Contents



Gail A. Sloan
 Niv E. Caviar
 Michael J.B. Tansey .
 11




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##### Table of Contents



Josefina T. Elchico.
 Tax and Accounting Implications
 Deductibility of Executive Compensation
 Role of Executives in Compensation Decisions
  Compensation Committee Report
  
 12




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##### Table of Contents



Summary Compensation Table
 Non-EquityStock
    
    Option
    
    Incentive Plan
    
    All OtherName and
    
    
    
    
    
    Salary
    
    
    
    
    
    Awards
    
    Awards
    
    Compensation
    
    Compensation
    
    TotalPrincipal Position
    
    Year
    
    ($)
    
    Bonus ($)
    
    ($) (1)
    
    ($) (1)
    
    ($) (2)
    
    ($)
    
    ($)Current OfficersDeirdre Y.
Gillespie, M.D.
    
    
    2008
    
    
    $
    402,600
    
    
    $
    
    
    
    $
    
    
    
    $
    1,093,763
    
    
    $
    200,772
    
    
    $
    
    
    
    $
    1,697,135President, Chief
    
    
    2007
    
    
    
    387,115
    
    
    
    
    
    
    
    
    
    
    
    1,016,876
    
    
    
    73,125
    
    
    
    
    
    
    
    1,477,116Executive Officer and
Assistant Secretary
    
    
    2006
    
    
    
    292,789
    
    
    
    50,000
    (3)
    
    
    
    
    
    
    727,872
    
    
    
    131,250
    
    
    
    61,770
    (4)
    
    
    1,263,681Gail A. Sloan
    
    
    2008
    
    
    
    196,906
    
    
    
    
    
    
    
    
    
    
    
    307,483
    
    
    
    53,609
    
    
    
    
    
    
    
    557,998Vice President of
    
    
    2007
    
    
    
    187,505
    
    
    
    
    
    
    
    
    
    
    
    332,201
    
    
    
    21,375
    
    
    
    
    
    
    
    541,081Finance and Secretary
    
    
    2006
    
    
    
    177,023
    
    
    
    44,256
    (5)
    
    
    
    
    
    
    313,259
    
    
    
    37,175
    
    
    
    
    
    
    
    571,713Former Officers*Niv E. Caviar (6)
    
    
    2008
    
    
    
    280,775
    
    
    
    
    
    
    
    
    
    
    
    226,995
    
    
    
    111,097
    
    
    
    25,000
    (9)
    
    
    643,867Executive Vice President,
Chief Business & Financial
Officer
    
    
    2007
    
    
    
    171,346
    (7)
    
    
    
    
    
    
    
    
    
    
    131,504
    
    
    
    23,461
    
    
    
    35,000
    (8)
    
    
    361,311Michael
Tansey, M.D., Ph.D.
    
    
    2008
    
    
    
    332,875
    
    
    
    
    
    
    
    
    
    
    
    387,029
    
    
    
    90,383
    
    
    
    
    
    
    
    810,287Executive Vice President
    
    
    2007
    
    
    
    325,000
    
    
    
    
    
    
    
    
    
    
    
    248,619
    
    
    
    48,750
    
    
    
    
    
    
    
    622,369and Chief Medical Officer
    
    
    2006
    
    
    
    95,733
    
    
    
    
    
    
    
    
    
    
    
    62,111
    
    
    
    22,484
    
    
    
    
    
    
    
    180,328Josefina T. Elchico
    
    
    2008
    
    
    
    219,823
    
    
    
    
    
    
    
    
    
    
    
    214,029
    
    
    
    69,125
    
    
    
    
    
    
    
    502,977Vice President of Quality
    
    
    2007
    
    
    
    206,895
    
    
    
    
    
    
    
    
    
    
    
    254,617
    
    
    
    31,209
    
    
    
    
    
    
    
    492,721Operations
    
    
    2006
    
    
    
    202,000
    
    
    
    50,500
    (5)
    
    
    
    
    
    
    202,128
    
    
    
    31,815
    
    
    
    
    
    
    
    486,443
 
 *
    
    These former officers were terminated on April 20, 2009 as part of the Companys restructuring
activities, as described above.(1)
    
    The amounts in this column reflect the dollar amount recognized for financial statement
reporting purposes for the fiscal years ended December 31, 2008 and December 31, 2007, in
accordance with SFAS 123(R) for awards and thus may include amounts from awards granted in and
prior to 2007. Assumptions used in the calculation of these amounts are included in footnote 1 to
our consolidated financial statements for the fiscal year ended December 31, 2008, included in our
Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 31, 2009.(2)
    
    These amounts represent the 2008 and 2007 performance-based bonus awards, which were paid in
fiscal year 2009 and 2008, respectively.(3)
    
    This amount represents a signing bonus paid to Dr. Gillespie in accordance with her employment
agreement, effective March 15, 2006.(4)
    
    This amount represents relocation expenses paid to Dr. Gillespie in accordance with her
employment agreement, effective March 15, 2006, including reimbursement for moving expenses of
$34,416, closing costs on the sale of her former residence of $9,629 and temporary living expenses
of $17,725.(5)
    
    These amounts represent retention bonuses paid in accordance with the Retention Agreements
dated as of October 6, 2005.(6)
    
    Mr. Caviar did not begin employment with us until 2007 and thus earned no compensation from us
in 2006.(7)
    
    On May 10, 2007, Mr. Caviar joined us as our Executive Vice President, Chief Business Officer
and Chief Financial Officer. Pursuant to his employment agreement,
Mr. Caviars initial base salary was
$275,000 per year.(8)
    
    This amount represents a relocation bonus paid to Mr. Caviar in accordance with his employment
agreement, effective May 10, 2007.(9)
    
    This amount represents a signing bonus paid to
Mr. Caviar in January 2008 in accordance with his
employment agreement. 13




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Grants of Plan-Based Awards Table  2008
 All OtherOptionAwards:Number of
    
    Exercise or
    
    Grant DateSecurities
    
    Base Price
    
    FairUnderlying
    
    of Option
    
    Value of StockGrant
    
    Options
    
    Awards
    
    and OptionName
    
    Date
    
    (#)
    
    ($ / Share)
    
    Awards ($)Current OfficersDeirdre Y. Gillespie
    
    
    2/21/2008
    
    
    
    150,000
    
    
    $
    2.42
    
    
    $
    297,060Gail A. Sloan
    
    
    2/21/2008
    
    
    
    25,000
    
    
    
    2.42
    
    
    
    49,510Former Officers*Niv E. Caviar
    
    
    2/21/2008
    
    
    
    50,000
    
    
    
    2.42
    
    
    
    99,020Michael J.B. Tansey
    
    
    2/21/2008
    
    
    
    40,000
    
    
    
    2.42
    
    
    
    79,2165/22/2008
    
    
    
    200,000
    
    
    
    1.82
    
    
    
    319,060Josefina T. Elchico
    
    
    2/21/2008
    
    
    
    25,000
    
    
    
    2.42
    
    
    
    49,510
 
 *
    
    These former officers were terminated on April 20, 2009. 14




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Outstanding Equity Awards at 2008 Fiscal Year End
 Number of
    
    Number ofSecurities
    
    SecuritiesUnderlying
    
    Underlying
    
    OptionUnexercised
    
    Unexercised
    
    Exercise
    
    OptionOptions
    
    Options
    
    Price
    
    Expiration(#)
    
    (#)
    
    ($)
    
    Date(1)Name
    
    Exercisable
    
    UnexercisableCurrent OfficersDeirdre Y. Gillespie
    
    
    566,667
    
    
    
    233,333
    (2)
    
    $
    5.26
    
    
    
    03/15/201668,750
    
    
    
    81,250
    (3)
    
    
    3.08
    
    
    
    02/05/201731,250
    
    
    
    118,750
    (3)
    
    
    2.42
    
    
    
    02/21/2018Gail A. Sloan
    
    
    3,687
    
    
    
    
    
    
    
    2.42
    
    
    
    09/28/2009359
    
    
    
    
    
    
    
    1.72
    
    
    
    11/02/2009972
    
    
    
    
    
    
    
    18.44
    
    
    
    01/28/20103,800
    
    
    
    
    
    
    
    35.00
    
    
    
    11/20/20103,000
    
    
    
    
    
    
    
    38.25
    
    
    
    07/19/20112,999
    
    
    
    
    
    
    
    35.50
    
    
    
    12/14/20115,999
    
    
    
    
    
    
    
    25.45
    
    
    
    07/18/20125,999
    
    
    
    
    
    
    
    29.50
    
    
    
    11/21/20125,999
    
    
    
    
    
    
    
    14.85
    
    
    
    05/12/20136,000
    
    
    
    
    
    
    
    23.55
    
    
    
    09/18/201314,000
    
    
    
    
    
    
    
    14.80
    
    
    
    05/21/201410,583
    
    
    
    
    
    
    
    2.40
    
    
    
    04/25/20155,415
    
    
    
    
    
    
    
    2.15
    
    
    
    05/19/201521,199
    
    
    
    
    
    
    
    4.20
    
    
    
    10/10/2015164,043
    
    
    
    20,505
    (4)
    
    
    4.46
    
    
    
    04/17/201611,458
    
    
    
    13,542
    (3)
    
    
    3.08
    
    
    
    02/05/20175,208
    
    
    
    19,792
    (3)
    
    
    2.42
    
    
    
    02/21/2018Former Officers*Niv E. Caviar
    
    
    71,250
    
    
    
    108,750
    (5)
    
    
    5.36
    
    
    
    05/10/201710,417
    
    
    
    39,583
    (3)
    
    
    2.42
    
    
    
    02/21/2018Michael J.B. Tansey
    
    
    91,028
    
    
    
    21,972
    (6)
    
    
    3.61
    
    
    
    07/17/201658,000
    
    
    
    29,000
    (6)
    
    
    3.23
    
    
    
    12/04/201619,792
    
    
    
    30,208
    (3)
    
    
    5.47
    
    
    
    05/23/20178,333
    
    
    
    31,667
    (3)
    
    
    2.42
    
    
    
    02/21/2018
    
    
    
    200,000
    (7)
    
    
    1.82
    
    
    
    05/22/2018Josefina T. Elchico
    
    
    10,000
    
    
    
    
    
    
    
    19.00
    
    
    
    10/12/20149,261
    
    
    
    
    
    
    
    2.40
    
    
    
    04/25/20154,739
    
    
    
    
    
    
    
    2.15
    
    
    
    05/19/201519,999
    
    
    
    
    
    
    
    4.20
    
    
    
    10/10/2015102,898
    
    
    
    12,862
    (4)
    
    
    4.46
    
    
    
    04/17/20168,708
    
    
    
    10,292
    (3)
    
    
    3.08
    
    
    
    02/05/20175,208
    
    
    
    19,792
    (3)
    
    
    2.42
    
    
    
    02/21/2018
 
 *
    
    These former officers were terminated on April 20, 2009.(1)
    
    All stock options expire ten years from the date of grant.(2)
    
    The stock options vest and become exercisable with respect to 200,000 of the underlying shares
on the one- year anniversary from the date of grant. Thereafter, 1/36th of the
remaining shares vest on a monthly basis over the next three years.(3)
    
    The stock options vest and become exercisable ratably on a monthly basis over four years from
the date of grant.(4)
    
    The stock options vest and become exercisable ratably on a monthly basis over three years from
the date of grant.(5)
    
    The stock options vest and become exercisable with respect to 25% of the underlying shares on
the one- year anniversary from the date of grant and with respect to an additional 75% of the
underlying shares ratably on a monthly basis over the next three years.(6)
    
    The stock options vest and become exercisable with respect to 33% of the underlying shares on
the one-year anniversary from the date of grant and with respect to an additional 67% of the
underlying shares ratably on a monthly basis over the next two years.(7)
    
    The options were to vest and become exercisable one business day if and after the Company
received written approval of its New Drug Application (NDA) for Riquent from the United States
Food and Drug Administration provided that such approval is within 18 months of the NDA filing.
The Company has since stopped the development of Riquent and does not expect to file an NDA for
this compound. 15




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Option Exercises and Stock Vested in Fiscal Year 2008
  Potential Payments Upon Termination or Change in Control
  ConstructiveTermination (1)or VoluntaryTerminationWithout
    
    
    with Good
    
    
    Change inName
    
    Cause
    
    
    Reason (2)
    
    
    ControlCurrent OfficersDeirdre Y. Gillespie
Severance (3)
    
    $
    608,400
    
    
    $
    608,400
    
    
    $
    benefits (4)
    
    
    5,406
    
    
    
    5,406
    
    
    
    stock options
    
    
    
    
    
    
    
    
    
    
    $
    613,806
    
    
    $
    613,806
    
    
    $
    Gail A. Sloan
severance (7)
    
    $
    198,551
    
    
    $
    
    
    
    $
    198,551benefits (8)
    
    
    4,815
    
    
    
    
    
    
    
    4,815stock options
    
    
    
    
    
    
    
    
    
    
    $
    203,366
    
    
    $
    
    
    
    $
    203,366Former Officers*Niv E. Caviar
severance (5)
    
    $
    211,613
    
    
    $
    211,613
    
    
    $
    211,613benefits (6)
    
    
    13,703
    
    
    
    13,703
    
    
    
    13,703stock options
    
    
    
    
    
    
    
    
    
    
    $
    225,316
    
    
    $
    225,316
    
    
    $
    225,316Michael J.B. Tansey
severance (5)
    
    $
    251,063
    
    
    $
    
    
    
    $
    251,063benefits (6)
    
    
    7,200
    
    
    
    
    
    
    
    7,200stock options
    
    
    
    
    
    
    
    
    
    
    $
    258,263
    
    
    $
    
    
    
    $
    258,263Josefina T. Elchico
severance (7)
    
    $
    222,624
    
    
    $
    
    
    
    $
    222,624benefits (8)
    
    
    12,792
    
    
    
    
    
    
    
    12,792stock options
    
    
    
    
    
    
    
    
    
    
    $
    235,416
    
    
    $
    
    
    
    $
    235,416
 16




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*
    
    As discussed in the CD&A, these former officers were terminated on April 20, 2009.(1)
    
    Per the Agreement, constructive termination shall mean: (i) a material reduction in the Chief
Executive Officers (the CEO) duties as an officer of us or a reduction in the CEOs title; (ii)
a relocation of the CEOs office to a location outside of San Diego County, California; (iii) any
material breach by us of our obligations under the Agreement; or (iv) any failure by us to obtain
the assumption of this Agreement by any successor or assign of us.(2)
    
    Per the employment agreement, voluntary termination with good reason shall mean: (a) Companys
material breach of his employment agreement; (b) Mr. Caviars position or job duties are modified
such that his duties are no longer consistent with the position of Chief Business Officer/Chief
Financial Officer or Chief Business Officer/Senior Commercial Executive or Senior Commercial
Executive; (c) Mr. Caviars position is modified such that his duties are no longer consistent with
an Executive Vice President level; or (d) Mr. Caviar no longer reports to the CEO.(3)
    
    Severance is equal to one and a half years of employees annual base salary at December 31,
2008.(4)
    
    Benefits include 12 months of medical coverage for the employee and her dependents.(5)
    
    Severance is equal to nine months of employees annual base salary at December 31, 2008.(6)
    
    Benefits include nine months of medical and dental coverage for the employee and his/her
dependents.(7)
    
    Severance is equal to one year of employees annual base salary at December 31, 2008.(8)
    
    Benefits include 12 months of medical and dental coverage for the employee and his/her
dependents. Director Compensation Table  2008
 Fees Earned orPaid in Cash
    
    Stock Awards
    
    Option Awards
    
    TotalName
    
    ($)
    
    ($)
    
    ($) (1)
    
    ($)Thomas H. Adams
    
    $
    35,750
    
    
    $
    
    
    
    $
    82,695
    
    
    $
    118,445Robert A. Fildes
    
    
    45,250
    
    
    
    
    
    
    
    82,695
    
    
    
    127,945Stephen M. Martin
    
    
    54,750
    
    
    
    
    
    
    
    82,695
    
    
    
    137,445Nader J. Naini (2)
    
    
    6,000
    
    
    
    
    
    
    
    26,642
    
    
    
    32,642Craig R. Smith
    
    
    64,250
    
    
    
    
    
    
    
    106,919
    
    
    
    171,169Martin P. Sutter
    
    
    
    
    
    
    
    
    
    
    39,465
    
    
    
    39,465James N. Topper
    
    
    10,250
    
    
    
    
    
    
    
    39,465
    
    
    
    49,715Frank E. Young
    
    
    34,500
    
    
    
    
    
    
    
    39,465
    
    
    
    73,965
 
 (1)
    
    The amounts in this column reflect the dollar amount recognized for financial statement
reporting purposes for the fiscal year ended December 31, 2008, in accordance with FAS 123(R) for
awards and thus may include amounts from awards granted in and prior to 2008. Assumptions used in
the calculation of these amounts are included in footnote 1 to our audited financial statements for
the fiscal year ended December 31, 2008, included in our Annual Report on Form 10-K filed with the
Securities and Exchange Commission on March 31, 2009.(2)
    
    Mr. Naini resigned as a director effective May 22, 2008. Director Compensation
 Retainers and Fees
 17




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##### Table of Contents



Option Grants Under the 2004 Plan
 
 Item 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER
MATTERS.
 Equity Compensation Plan Information
  Number ofSecuritiesRemaining Available forNumber of
    
    
    
    
    
    Future Issuance UnderSecurities to be
    
    Weighted-
    
    EquityIssued upon
    
    Average Exercise
    
    CompensationExercise of
    
    Price of
    
    Plans (ExcludingOutstanding
    
    Outstanding
    
    SecuritiesOptions, Warrants
    
    Options, Warrants
    
    Reflected inand Rights
    
    and Rights
    
    Column (a))Plan CategoryEquity Compensation
plans approved by
security holders
    
    
    5,626,959
    (1)
    
    $
    6.80
    
    
    
    1,259,410
    (2)Equity Compensation
plans not approved
by security holders
    
    
    
    
    
    
    
    
    
    
    
 
 (1)
    
    Outstanding options to purchase shares of our common stock under the La Jolla
Pharmaceutical Company 1994 Stock Incentive Plan and the 2004 Plan.(2)
    
    Includes 1,242,433 shares subject to the 2004 Plan and 16,977 shares subject to the
1995 Plan (each stated as of December 31, 2008). 18




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##### Table of Contents



Security Ownership of Certain Beneficial Owners and Management
  
    
    each person who is known by us to be the beneficial owner of more than 5% of our
common stock;
    
    each of our directors;
    
    each of our named executive officers listed in the summary compensation table; and
    
    all of our directors and executive officers as a group.
 Amount and Nature ofName and Address of
    
    Nature of Beneficial
    
    
    Percent ofBeneficial Owner1
    
    Ownership2
    
    
    Class (%)3BioMarin Pharmaceutical, Inc.
    
    
    10,173,120
    (4)
    
    
    15.5105 Digital Drive
Novato, California 94949Essex Woodlands Health Ventures Fund VI, L.P. and
    
    
    6,361,446
    (5)(6)
    
    
    9.1Essex Woodlands Health Ventures Fund VII, L.P.
10001 Woodloch Forest Drive, Suite 175
The Woodlands, Texas 77380Thomas H. Adams, Ph.D.
    
    
    119,758
    (7)
    
    
    
    *Robert A. Fildes, Ph.D.
    
    
    102,346
    (8)
    
    
    
    *Deirdre Y. Gillespie, M.D.
    
    
    803,125
    (9)
    
    
    1.2Stephen M. Martin
    
    
    105,440
    (10)
    
    
    
    *Craig R. Smith, M.D.
    
    
    123,400
    (11)
    
    
    
    *Martin P. Sutter
    
    
    6,512,526
    (12)
    
    
    9.3James N. Topper, M.D., Ph.D.
    
    
    1,297,844
    (13)
    
    
    1.9Frank E. Young, M.D., Ph.D.
    
    
    43,600
    (14)
    
    
    
    *Niv E. Caviar
    
    
    296,523
    (15)
    
    
    
    *Josefina T. Elchico
    
    
    238,759
    (16)
    
    
    
    *Gail A. Sloan
    
    
    309,633
    (17)
    
    
    
    *Michael J.B. Tansey, M.D., Ph.D.
    
    
    552,037
    (18)
    
    
    
    *All current directors and executive officers as a group (9 persons)
    
    
    9,417,672
    (19)
    
    
    12.9
 
 *
    
    Less than 1%.(1)
    
    Unless otherwise indicated, the address for each beneficial owner is care of La Jolla
Pharmaceutical Company, 6455 Nancy Ridge Drive, San Diego, California 92121.(2)
    
    The table above includes the number of shares underlying options and warrants that are
exercisable within 60 days from March 31, 2009. All information with respect to beneficial
ownership is based upon filings made by the respective beneficial owners with the Securities
and Exchange Commission or information provided to the Company by such beneficial owners.
Except as indicated in the footnotes to this table, the persons named in the table have sole
voting and investment power with respect to all shares of common stock shown as beneficially
owned by them, subject to community property laws.(3)
    
    On April 24, 2009, there were 65,722,648 shares of common stock outstanding. Shares not
outstanding that are subject to options and warrants exercisable by the holder thereof within
60 days of April 24, 2009 are deemed outstanding for the purposes of calculating the number
and percentage owned by such stockholder, but not deemed outstanding for the purpose of
calculating the percentage owned by each other stockholder listed.(4)
    
    In connection with the development agreement dated January 4, 2009 between us and BioMarin CF
(a wholly-owned subsidiary of BioMarin Pharmaceutical, Inc.), we entered into a securities
purchase agreement with BioMarin Pharmaceutical, Inc. dated January 4, 2009 whereby we sold
339,104 shares of Series B-1 Preferred Stock to BioMarin Pharmaceutical, Inc. at a price per
share of $22.1171. On March 27, 2009, in connection with the termination of the development agreement, the Series B-1 Preferred Stock converted into
the right to receive 10,173,120 shares of common stock. These shares were issued on April 22,
2009. 19




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##### Table of Contents



(5)
    
    Based on filings made by Essex Woodlands Health Ventures Funds, including the Schedule 13D
filed on December 23, 2005 and Forms 4 filed on April 12, 2007, May 14, 2008 and February 26,
2009, respectively. Includes warrants to purchase 4,139,014 shares of common stock that are
exercisable within 60 days.(6)
    
    Share numbers reported in the Schedule 13D, as applicable, have been adjusted to reflect the
five-for-one reverse stock split effective December 21, 2005.(7)
    
    Includes 118,358 shares subject to options that are exercisable within 60 days.(8)
    
    Includes 102,346 shares subject to options that are exercisable within 60 days.(9)
    
    Includes 803,125 shares subject to options that are exercisable within 60 days.(10)
    
    Includes 105,400 shares subject to options that are exercisable within 60 days.(11)
    
    Includes 123,400 shares subject to options that are exercisable within 60 days.(12)
    
    Includes 113,080 shares owned by Mr. Sutter, 38,000 shares subject to options that are
exercisable within 60 days, and 6,361,446 shares beneficially owned by Essex Woodlands Health
Ventures Fund VI, L.P. and Essex Woodlands Health Ventures Fund VII, L.P. Mr. Sutter is a
Managing Director of these funds. Except for his pecuniary interest therein, Mr. Sutter
disclaims all beneficial ownership in the shares owned by Essex Woodlands Health Ventures Fund
VI L.P. and Essex Woodlands Health Ventures Fund VII, L.P.(13)
    
    Includes 38,000 shares subject to options that are exercisable within 60 days and 1,259,844
shares beneficially owned by Frazier Healthcare V L.P., of which Dr. Topper is a General
Partner. Except for his pecuniary interest therein, Dr. Topper disclaims all beneficial
ownership in the shares owned by Frazier Healthcare V, L.P.(14)
    
    Includes 38,000 shares subject to options that are exercisable within 60 days.(15)
    
    Includes 285,000 shares subject to options that are exercisable within 60 days.(16)
    
    Includes 238,759 shares subject to options that are exercisable within 60 days.(17)
    
    Includes 300,079 shares subject to options that are exercisable within 60 days.(18)
    
    Includes 535,000 shares subject to options that are exercisable within 60 days.(19)
    
    Includes 1,666,708 shares subject to options that are exercisable within 60 days and warrants
to purchase 5,398,858 shares of common stock that are exercisable within 60 days.
 
 Item 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE.
 Compensation Committee Interlocks and Insider Participation
  Review and Approval of Related Party-Transactions
  20




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##### Table of Contents



Related-Party Transactions
  
 Item 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES.
  2007
    
    
    2008Audit Fees
    
    $
    272,386
    
    
    $
    298,861Audit Related Fees
    
    
    
    
    
    
    Tax Fees
    
    
    21,800
    
    
    
    87,000All Other Fees
    
    
    
    
    
    
    45,000Total
    
    $
    294,186
    
    
    $
    430,861
 Audit Fees
 Tax Fees
 All Other Fees.
 Pre-approval Policy
 21




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##### Table of Contents



PART IV
 
 Item 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES.
  Exhibit Number
    
    Description31.1
    
    Certification of Principal Executive Officer Pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 200231.2
    
    Certification of Principal Financial Officer Pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 2002
 22




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##### Table of Contents



SIGNATURES
  LA JOLLA PHARMACEUTICAL COMPANYApril 30, 2009
    By:
    /s/ Deirdre Y. GillespieDeirdre Y. Gillespie, M.D.President, Chief Executive Officer and
Assistant Secretary 23




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##### Table of Contents



EXHIBIT INDEX
 Exhibit Number
    
    Description31.1
    
    Certification of Principal Executive Officer Pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 200231.2
    
    Certification of Principal Financial Officer Pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 2002