Ownership Submission
FORM 3
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

INITIAL STATEMENT OF BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
OMB APPROVAL
OMB Number: 3235-0104
Expires: January 31, 2005
Estimated average burden hours per response... 0.5

(Print or Type Responses)
1. Name and Address of Reporting Person *
  GILEAD SCIENCES INC
2. Date of Event Requiring Statement (Month/Day/Year)
10/25/2006
3. Issuer Name and Ticker or Trading Symbol
ACHILLION PHARMACEUTICALS INC [ACHN]
(Last)
(First)
(Middle)
333 LAKESIDE DRIVE
4. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
_____ Director __X__ 10% Owner
_____ Officer (give title below) _____ Other (specify below)
5. If Amendment, Date Original Filed(Month/Day/Year)
(Street)

FOSTER CITY, CA 94404
6. Individual or Joint/Group Filing(Check Applicable Line)
_X_ Form filed by One Reporting Person
___ Form filed by More than One Reporting Person
(City)
(State)
(Zip)
Table I - Non-Derivative Securities Beneficially Owned
1.Title of Security
(Instr. 4)
2. Amount of Securities Beneficially Owned
(Instr. 4)
3. Ownership Form: Direct (D) or Indirect (I)
(Instr. 5)
4. Nature of Indirect Beneficial Ownership
(Instr. 5)

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly. SEC 1473 (7-02)
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB control number.

Table II - Derivative Securities Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security
(Instr. 4)
2. Date Exercisable and Expiration Date
(Month/Day/Year)
3. Title and Amount of Securities Underlying Derivative Security
(Instr. 4)
4. Conversion or Exercise Price of Derivative Security 5. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 5)
6. Nature of Indirect Beneficial Ownership
(Instr. 5)
Date Exercisable Expiration Date Title Amount or Number of Shares
Series C-1 Convertible Preferred Stock   (1)   (2) Common Stock 370,494 (3) (4) $ (3) D  
Series C-2 Convertible Preferred Stock   (1)   (2) Common Stock 745,345 (3) (4) $ (3) D  

Reporting Owners

Reporting Owner Name / Address Relationships
Director 10% Owner Officer Other
GILEAD SCIENCES INC
333 LAKESIDE DRIVE
FOSTER CITY, CA 94404
    X    

Signatures

/s/ John F. Milligan, Executive Vice President and Chief Financial Officer 10/25/2006
**Signature of Reporting Person Date

Explanation of Responses:

* If the form is filed by more than one reporting person, see Instruction 5(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
(1) These shares will automatically convert into common stock upon the closing of the issuer's initial public offering of common stock.
(2) Not applicable.
(3) Reflects a 1-for-8 reverse stock split, which became effective on October 24, 2006. Upon the closing of the issuer's initial public offering, each share of Series C-1 Convertible Preferred Stock will convert into approximately 0.149 shares of common stock and each share of Series C-2 Convertible Preferred Stock will convert into approximately 0.125 shares of common stock.
(4) Includes shares of preferred stock issued as a dividend which will be paid upon the conversion of the preferred stock.

Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, See Instruction 6 for procedure.

Potential persons who are to respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB number.