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
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(Print or Type Responses)
1. Name and Address of Reporting Person *
  RA Capital Healthcare Fund LP
 2. Date of Event Requiring Statement (Month/Day/Year)
09/30/2013		 3. Issuer Name and Ticker or Trading Symbol
ACHILLION PHARMACEUTICALS INC [ACHN]
(Last)
(First)
(Middle)
C/O RA CAPITAL MANAGEMENT, LLC, 20 PARK PLAZA, SUITE 1200		 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)

BOSTON, MA 02116		 6. Individual or Joint/Group Filing(Check Applicable Line)
___ Form filed by One Reporting Person
_X_ 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)
Common Stock, $0.001 par value (1) 11,657,061
I
See Footnote (2) (3)

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly. SEC 1473 (7-02)
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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

Reporting Owners

Reporting Owner Name / Address Relationships
Director 10% Owner Officer Other
RA Capital Healthcare Fund LP
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116		     X    
RA CAPITAL MANAGEMENT, LLC
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116		     X    
Kolchinsky Peter
C/O RA CAPITAL MANAGEMENT, LLC
20 PARK PLAZA, SUITE 1200
BOSTON, MA 02116		     X    

Signatures

/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC 10/04/2013
**Signature of Reporting Person Date
/s/ Peter Kolchinsky, individually 10/04/2013
**Signature of Reporting Person Date
/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC, the General Partner of RA Capital Healthcare Fund, L.P. 10/04/2013
**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 securities include 8,944,255 shares held by RA Capital Healthcare Fund, L.P. (the "Fund") and 2,712,806 shares held in an account owned by Blackwell Partners, LLC (the "Blackwell Account").
(2) RA Capital Management, LLC (the "Adviser") is the general partner of the Fund and the investment adviser of the Blackwell Account. Peter Kolchinsky is the sole manager of the Adviser. In their respective capacities, each of Mr. Kolchinsky and the Adviser may be deemed to beneficially own the reported securities.
(3) Pursuant to Rule 16a-1 under the Securities Exchange Act of 1934, as amended (the "Act"), each of the Reporting Persons disclaims beneficial ownership of the securities reported herein except to the extent of their respective pecuniary interests therein. The filing of this Form 4 shall not be construed as an admission that Mr. Kolchinsky or the Adviser is or was for the purposes of Section 16(a) of the Act, or otherwise, the beneficial owner of any of securities reported herein.

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