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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, DC 20549
 FORM 10-Q
 QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d)
OF THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period ended: September 30, 2006
 Commission file number: 1-10827
 PAR PHARMACEUTICAL COMPANIES, INC.
  Delaware
(State or other jurisdiction of 
incorporation or organization)
    
    22-3122182
(I.R.S. Employer
Identification No.)300 Tice Boulevard, 
Woodcliff Lake, New Jersey
(Address of principal executive offices)
    
    07677
(Zip Code)
   o þ
   Large accelerated filer  þ
    
    Accelerated filer  o
    
    Non-accelerated filer  o
  o þ




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TABLE OF CONTENTS
PAR PHARMACEUTICAL COMPANIES, INC.
FORM 10-Q
FOR THE FISCAL QUARTER ENDED SEPTEMBER 30, 2006
 PAGEPART I   FINANCIAL INFORMATIONItem 1. Financial Statements
    
    
    2Item 2. Managements Discussion and Analysis of Financial Condition
and Results of Operations
    
    
    2Item 3. Quantitative and Qualitative Disclosures About Market Risk
    
    
    2Item 4. Controls and Procedures
    
    
    4PART II   OTHER INFORMATIONItem 1. Legal Proceedings
    
    
    4Item 1A. Risk Factors
    
    
    9Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    12Item 5.
Other Information
    
    
    12Item 6. Exhibits
    
    
    12SIGNATURES
    
    
    14EMPLOYMENT AGREEMENT BY & BETWEEN PAR PHARMACEUTICAL COMPANIES AND PATRICK LEPORESEPARATION AGREEMENT BY & BETWEEN PAR PHARMACEUTICALS & MARK AUERBACHSEPARATION AGREEMENT BY & BETWEEN PAR PHARMACEUTICALS & MICHAEL GRAVESSEPARATION AGREEMENT BY & BETWEEN PAR PHARMACEUTICALS & SHANKAR HARIHARANCERTIFICATION OF THE PRINCIPAL EXECUTIVE OFFICERCERTIFICATION OF THE PRINCIPAL FINANCIAL OFFICERCERTIFICATION BY THE CHIEF EXECUTIVE OFFICERCERTIFICATION BY THE CHIEF FINANCIAL OFFICER




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PART I  FINANCIAL INFORMATION
  
 ITEM 1. Financial Statements
  
 ITEM 2. Managements Discussion and Analysis of Financial Condition and Results of
Operations
  
 ITEM 3. Quantitative and Qualitative Disclosures About Market Risk
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September 30,
    
    
    December 31,2006
    
    
    2005Estimated Fair
    
    
    Estimated FairValue
    
    
    ValueSecurities issued by U.S. government and agencies
    
    $
    75,137
    
    
    $
    79,886Debt securities issued by various state and local municipalities and agencies
    
    
    13,749
    
    
    
    13,721Other marketable debt securities
    
    
    14,522
    
    
    
    13,200Total marketable debt securities
    
    
    103,408
    
    
    
    106,807Marketable equity securities available for sale
    
    
    6,000
    
    
    
    1,380Total
    
    $
    109,408
    
    
    $
    108,187
 Available for Sale Securities:
    ®
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ITEM 4. Controls and Procedures
  
 PART II  OTHER INFORMATION
 
 ITEM 1. Legal Proceedings
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Contractual Matters
 Ò
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Patent Related Matters
  Roxane Roxane
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®
    Industry Related Matters
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ITEM 1A. Risk Factors
  Risks that Relate to the registrants Accounting and Internal Controls
 The registrant must restate its financial statements as of December 31, 2005 and 2004 and for each
of the three years in the period ended December 31, 2005, as well as restate selected financial
data as of and for each of the five years in the period ended December 31, 2005. The registrant
will also restate quarterly results of operations for each of the two years in the period ended
December 31, 2005. The registrant will also restate the first quarter of 2006. The restatement
process is not yet complete. nvestors should not rely on such prior financial statements until they
are restated and filed with the Commission.
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The registrant likely has material weaknesses in its internal control over financial reporting.
 significant deficiency material weakness
  As a result of the required restatement, material information concerning the registrants operating
results and financial condition is not available and is not expected to be available at any certain
time.
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The registrant may lose existing customers or may not be successful in gaining new customers or
commercial relationships as a result of the issues relating to the restatement of the Prior
Financial Statements, its internal controls and related matters.
  The registrant has received a notice of purported default and notice of acceleration with respect
to its convertible notes and a lawsuit has been commenced.
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ITEM 2.  Unregistered Sales of Equity Securities and Use of Proceeds
 Issuer Purchases of Equity Securities(1)  Quarter Ending September 30, 2006
 Total Number ofShares of
    
    Maximum NumberAverage
    
    Common Stock
    
    of Shares ofPrice Paid
    
    Purchased as
    
    Common Stock thatTotal Number of
    
    per Share
    
    Part of Publicly
    
    May Yet BeShares of
    
    of
    
    Announced
    
    Purchased UnderCommon Stock
    
    Common
    
    Plans or
    
    the Plans orPeriod
    
    Purchased
    
    Stock
    
    Programs
    
    Programs(2)July 2, 2006
through July 29,
2006
    
    
    
    
    
    
    N/A
    
    
    
    
    
    
    
    977,083July 30, 2006
through August 26,
2006
    
    
    
    
    
    
    N/A
    
    
    
    
    
    
    
    977,083August 27, 2006
through September
30, 2006
    
    
    
    
    
    
    N/A
    
    
    
    
    
    
    
    977,083
 (1)
    
    In April 2004, the Board authorized the repurchase of up to $50,000 of the registrants
common stock. Repurchases are made, subject to compliance with applicable securities laws,
from time to time in the open market or in privately negotiated transactions, whenever it
appears prudent to do so. Shares of common stock acquired through the repurchase program are
available for reissuance for general corporate purposes. The authorized amount remaining for
stock repurchases under the repurchase program is $17.8 million. The repurchase program has no
expiration date.(2)
    
    Based on the closing price of the registrants common stock on The New York Stock Exchange
$18.24 at September 29, 2006.
 
 Item 5. Other Information
   
 ITEM 6. Exhibits
 10.1
    
    
    Employment agreement by and between Par
Pharmaceutical Companies, Inc. and Patrick
LePore, dated as of November 10, 2006.10.2
    
    
    Separation agreement by and between Par
Pharmaceutical Companies, Inc. and Mark
Auerbach, dated as of December 1, 2006.10.3
    
    
    Separation agreement by and between Par
Pharmaceutical Companies, Inc. and Michael
Graves, dated as of November 10, 2006.10.4
    
    
    Separation agreement by and between Par
Pharmaceutical Companies, Inc. and Shankar
Hariharan, dated as of November 29, 2006.31.1
    
    
    Certification of the Principal Executive Officer.31.2
    
    
    Certification of the Principal Financial Officer.32.1
    
    
    Certification by the Chief Executive Officer
pursuant to 18 U.S.C. Section 1350, as adopted
pursuant to Section 906 of the Sarbanes-Oxley
Act of 2002.* (To be attached)32.2
    
    
    Certification by the Chief Financial Officer
pursuant to 18 U.S.C. Section 1350, as adopted
pursuant to Section 906 of the Sarbanes-Oxley
Act of 2002.* (To be attached)
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*
    
    The certifications to be furnished as Exhibits 32.1 and 32.2 to
the registrants Quarterly Report on Form 10-Q/A will not be
deemed to be filed with the SEC and will not be incorporated by
reference into any filing of the registrant under the Securities
Act of 1933, as amended, or the Securities Act of 1934, as
amended, whether made before or after the date of this Quarterly
Report on Form 10-Q, irrespective of any general incorporation
language contained in any such filing.
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SIGNATURES
  PAR PHARMACEUTICAL COMPANIES, INC.
(registrant)Date:  December 21, 2006
    /s/      Patrick G. LePorePatrick G. LePorePresident and Chief Executive OfficerDate:  December 21, 2006
    /s/ Gerard A. MartinoGerard A. MartinoExecutive Vice President and Chief
Financial Officer 14




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EXHIBIT INDEX
 10.1
    
    
    Employment agreement by and between Par Pharmaceutical
Companies, Inc. and Patrick LePore, dated as of November 10,
2006.10.2
    
    
    Separation agreement by and between Par Pharmaceutical
Companies, Inc. and Mark Auerbach, dated as of December 1,
2006.10.3
    
    
    Separation agreement by and between Par Pharmaceutical
Companies, Inc. and Michael Graves, dated as of November 10,
2006.10.4
    
    
    Separation agreement by and between Par Pharmaceutical
Companies, Inc. and Shankar Hariharan, dated as of November
29, 2006.31.1
    
    
    Certification of the Principal Executive Officer.31.2
    
    
    Certification of the Principal Financial Officer.32.1
    
    
    Certification by the Chief Executive Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.*32.2
    
    
    Certification by the Chief Financial Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.*
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