<PAGE>

   As filed with the Securities and Exchange Commission on December 26, 2006

================================================================================

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                 ---------------

                                    FORM S-8
             REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933
                                 ---------------

                                 PolyMedix, Inc.
             (Exact Name of Registrant as Specified in Its Charter)
                               Delaware 27-0125925
      (State or Other Jurisdiction (I.R.S. Employer Identification Number)
                         of Incorporation or Operation)
                      170 N. Radnor-Chester Road, Suite 300
                           Radnor, Pennsylvania 19087
          (Address of Principal Executive Offices, including Zip Code)
                   ------------------------------------------
              PolyMedix, Inc. 2005 Omnibus Equity Compensation Plan
          PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan
                            (Full Title of the Plan)
                   -------------------------------------------
                                Nicholas Landekic
                      President and Chief Executive Officer
                      170 N. Radnor-Chester Road, Suite 300
                           Radnor, Pennsylvania 19087
                                 (484) 598-2400
 (Name, Address And Telephone Number, Including Area Code, of Agent For Service)
                 ----------------------------------------------
                          Copies of communications to:
                                Jeffrey P. Libson
                               Pepper Hamilton LLP
                                 400 Berwyn Park
                                899 Cassatt Road
                                Berwyn, PA 19312
                                 (610) 640-7800
                 ----------------------------------------------
                         CALCULATION OF REGISTRATION FEE
<TABLE>
<CAPTION>

=====================================================================================================================
                                                   Proposed maximum        Proposed maximum
     Title of shares to be       Amount to be     offering price per      aggregate offering         Amount of
          registered            registered (1)          share                   price             registration fee
---------------------------------------------------------------------------------------------------------------------
<S>                                <C>                   <C>                  <C>                          <C>
Common Stock ($0.001 par value)    1,116,000(2)          $3.25(3)             $3,627,000                   $389
---------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par value)    2,884,000(4)          $1.50(3)             $4,326,000                   $463
---------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par value)    1,423,000(5)          $1.50(3)             $2,134,500                   $229
=====================================================================================================================
</TABLE>

--------------------------------------------------------------------------------
(1) Pursuant to Rule 416(b), there shall also be deemed covered hereby any
additional securities that may hereinafter be offered or issued to prevent
dilution resulting from stock splits, stock dividends, recapitalizations or
certain other capital adjustments.

(2) Consists of shares issuable under the PolyMedix, Inc. 2005 Omnibus Equity
Compensation Plan.

(3) Estimated solely for the purposes of calculating the registration fee in
accordance with Rule 457(h)(1) and (c) under the Securities Act of 1933. As to
shares subject to outstanding but unexercised options, the price and fee are
computed based upon the weighted average exercise price of $1.50 per share. As
to the 30,000 shares issued pursuant to grants of common stock pursuant to the
2005 Omnibus Equity Compensation Plan, the price and fee are based on the value
per share on the date of grant, which was $1.50 in all cases. As to the
remaining shares, the price and fee are computed based upon $3.25 per share, the
average of the high and low prices for the common stock reported on the
Over-the-Counter Bulletin Board on December 21, 2006.
<PAGE>

(4) Consists of shares purchasable upon exercise of options outstanding to
purchase common stock as well as grants of common stock issued and outstanding,
both as of the date hereof, under the 2005 Omnibus Equity Compensation Plan. The
amount of shares issuable pursuant to such options may again become available
for grant and issuance in the event the outstanding options expire or are
forfeited prior to being exercised.


(5) Consists of shares purchasable upon exercise of options outstanding to
purchase common stock under the 2002 Equity Compensation Plan.

<PAGE>


                                     PART I
              INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

Item 1.  Plan Information.

       The document(s) containing the information specified in Part I of Form
S-8 will be sent or given to participants in the Plans as specified by Rule
428(b)(1) of the Securities Act of 1933, as amended (the "Securities Act"). Such
documents are not being filed with the Securities and Exchange Commission (the
"Commission"), but constitute, along with the documents incorporated by
reference into this Registration Statement, a prospectus that meets the
requirements of Section 10(a) of the Securities Act.

Item 2.  Registrant Information and Employee Plan Annual Information.

       PolyMedix, Inc. (the "Registrant" or "Small Business Issuer") will
furnish without charge to each person to whom the prospectus is delivered, upon
the written or oral request of such person, a copy of any and all of the
documents incorporated by reference, other than exhibits to such documents
(unless such exhibits are specifically incorporated by reference to the
information that is incorporated). Requests should be directed to PolyMedix,
Inc., 170 N. Radnor Chester Road, Suite 300, Radnor, Pennsylvania 19087,
Attention: Edward F. Smith, Vice President, Chief Financial Officer and
Secretary; telephone number (484) 598-2332.


                                     PART II
               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  Incorporation of Documents by Reference.

         The following documents which have been filed by the Registrant with
the Commission are incorporated by reference into this Registration Statement:

         (a) The Registrant's Annual Registration Statement on Form 10-SB
(Registration No. 333-51895) filed with the Commission on April 5, 2006 (as
amended by Amendment No. 1 filed with the Commission on May 24, 2006 and
Amendment No. 2 filed with the Commission on June 19, 2006 and collectively, the
"Registration Statement on Form 10-SB"); Quarterly Report on Form 10-QSB for the
quarter ended June 30, 2006 filed with the Commission on August 14, 2006;
Quarterly Report on Form 10-QSB for the quarter ended September 30, 2006 filed
with the Commission on November 13, 2006; Current Report on Form 8-K filed with
the Commission on August 1, 2006; Current Report on Form 8-K filed with the
Commission on November 13, 2006; Current Report on Form 8-K filed with the
Commission on November 15, 2006; and Current Report on December 20, 2006.

         (b) The description of the Registrant's Common Stock contained in the
Registrant's Registration Statement on Form 10-SB filed, including any
amendments or reports filed for the purpose of updating such description in
which there is described the terms, rights and provisions applicable to the
Registrant's Common Stock.

         All documents filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), after the date hereof and prior to the filing of a
post-effective amendment which indicates that all securities offered pursuant to
this Registration Statement have been sold or which deregisters all securities
then remaining unsold shall be deemed to be incorporated by reference herein and
to be a part hereof from the date of filing of such documents.

Item 4.  Description of Securities.

         Not applicable.


<PAGE>

Item 5.  Interests of Named Experts and Counsel.

         Not applicable.

Item 6.  Indemnification of Directors and Officers.


       Section 102 of the General Corporation Law of the State of Delaware
permits a corporation to eliminate the personal liability of directors of a
corporation to the corporation or its stockholders for monetary damages for a
breach of fiduciary duty as a director, except where the director breached his
duty of loyalty, failed to act in good faith, engaged in intentional misconduct
or knowingly violated a law, authorized the payment of a dividend or approved a
stock repurchase in violation of Delaware corporate law or obtained an improper
personal benefit. The Registrant's Amended and Restated Certificate of
Incorporation, as amended, provides that a director of the Registrant shall not
be personally liable to it or its stockholders for monetary damages for any
breach of fiduciary duty as a director, except to the extent that such exemption
from liability or limitation thereof is not permitted under the General
Corporation Law of the State of Delaware as currently in effect or as the same
may hereafter be amended.

       Section 145 of the General Corporation Law of the State of Delaware
provides that a corporation has the power to indemnify a director, officer,
employee, or agent of the corporation and other persons serving at the request
of the corporation in related capacities against expenses (including attorneys'
fees), judgments, fines and amounts paid in settlements actually and reasonably
incurred by the person in connection with an action, suit or proceeding to which
he is or is threatened to be made a party by reason of such position, if such
person acted in good faith and in a manner he reasonably believed to be in or
not opposed to the best interests of the corporation, and, in any criminal
action or proceeding, had no reasonable cause to believe his conduct was
unlawful, except that, in the case of actions brought by or in the right of the
corporation, no indemnification shall be made with respect to any claim, issue
or matter as to which such person shall have been adjudged to be liable to the
corporation unless and only to the extent that the Court of Chancery or other
adjudicating court determines that, despite the adjudication of liability but in
view of all of the circumstances of the case, such person is fairly and
reasonably entitled to indemnify for such expenses which the Court of Chancery
or such other court shall deem proper.

       The Registrant's Amended and Restated Certificate of Incorporation
provides that the Registrant will indemnify and advance expenses upon request to
any person who is or was a party or threatened to be made a party to any
threatened, pending or completed action, suit, proceeding or claim, whether
civil, criminal, administrative or investigative, by reason of the fact that he
or she is or was or has agreed to become, a director, officer or employee of the
Registrant or, at the election of the Registrant's board of directors, an agent
of the Registrant or is or was serving at the request of the Registrant as a
director, officer or employee or, at the election of the Registrant's board or
directors, agent of any other corporation, partnership, joint venture, trust or
other enterprise against any and all expenses (including attorneys' fees),
judgments, fines, penalties and amounts paid in settlement or incurred in
connection with the investigation, preparation to defend or defense or such
action, suit, proceeding or claim.

       The Registrant has purchased certain liability insurance for its officers
and directors.

Item 7.  Exemption From Registration Claimed.

         Not applicable.

Item 8.  Exhibits.

         4.1      PolyMedix, 2005 Omnibus Equity Compensation Plan.

         4.2      PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan.

         5.1      Opinion of Pepper Hamilton LLP as to the validity of the
                  securities being registered.

         23.1     Consent of Deloitte & Touche LLP.
<PAGE>

         23.2     Consent of Pepper Hamilton LLP (included in Exhibit 5.1
                  hereto).

         24.1     Powers of Attorney (included on the signature page hereto).

Item 9.  Undertakings.

         (a) The undersigned Small Business Issuer hereby undertakes, pursuant
to Item 512 of Regulation S-B:

                  (1) To file, during any period in which offers or sales are
                  being made, a post-effective amendment to this Registration
                  Statement:

                  (i)   To include any prospectus required by Section 10(a)(3)
                        of the Securities Act of 1933.

                  (ii)  To reflect in the prospectus any facts or events which,
                        individually or together, represent a fundamental change
                        in the information in the Registration Statement.
                        Notwithstanding the foregoing, any increase or decrease
                        in volume of securities offered (if the total dollar
                        value of securities offered would not exceed that which
                        was registered) and any deviation from the low or high
                        end of the estimated maximum offering range may be
                        reflected in the form of prospectus filed with the
                        Securities and Exchange Commission pursuant to Rule
                        424(b) if, in the aggregate, the changes in volume and
                        price represent no more than a 20% change in the maximum
                        aggregate offering price set forth in the "Calculation
                        of Registration Fee" table in the effective Registration
                        Statement.

                  (iii) To  include   any   additional   or   changed   material
                        information on the plan of distribution.

                        Provided, however, that paragraphs (a)(1)(i) and (a)(1)
                        (ii) do not apply if the information required to be
                        included in a post-effective amendment by those
                        paragraphs is contained in periodic reports filed by the
                        Registrant pursuant to Section 13 or Section 15(d) of
                        the Securities Exchange Act of 1934 that are
                        incorporated by reference in the Registration Statement.

                  (2) For determining any liability under the Securities Act of
                  1933, treat each such post-effective amendment as a new
                  registration statement of the securities offered, and the
                  offering of the securities at that time shall be deemed to be
                  the initial bona fide offering.

                  (3) File a post-effective amendment to remove from
                  registration any of the securities being registered that
                  remain unsold at the end of the offering.

                  (4) For determining liability of the undersigned Small
                  Business Issuer under the Securities Act to any purchaser in
                  the initial distribution of securities, the undersigned Small
                  Business Issuer undertakes that in a primary offering of
                  securities of the undersigned Small Business Issuer pursuant
                  to this Registration Statement, regardless of the underwriting
                  method used to sell the securities to the purchaser, if the
                  securities are offered or sold to such purchaser by means of
                  any of the following communications, the undersigned Small
                  Business Issuer will be a seller to the purchaser and will be
                  considered to offer or sell such securities to such purchaser:

                  (i)   Any preliminary prospectus or prospectus of the
                        undersigned Small Business Issuer relating to the
                        offering required to be filed pursuant to Rule 424;

                  (ii)  Any free writing prospectus relating to the offering
                        prepared by or on behalf of the undersigned Small
                        Business Issuer or used or referred to by the
                        undersigned Small Business Issuer;
<PAGE>

                  (iii) The portion of any other free writing prospectus
                        relating to the offering containing material information
                        about the undersigned Small Business Issuer or its
                        securities provided by or on behalf of the undersigned
                        Small Business Issuer; and

                  (iv)  Any other communication that is an offer in the offering
                        made by the undersigned Small Business Issuer to the
                        purchaser.

         (e) Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the Small
Business Issuer has been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Securities Act and is, therefore, unenforceable. In the event that a
claim for indemnification against such liabilities (other than the payment by
the registrant of expenses incurred or paid by a director, officer or
controlling person of the registrant in the successful defense of any action,
suit or proceeding) is asserted by such director, officer or controlling person
in connection with the securities being registered, the Small Business Issuer
will, unless in the opinion of its counsel the matter has been settled by
controlling precedent, submit to a court of appropriate jurisdiction the
question whether such indemnification by it is against public policy as
expressed in the Securities Act and will be governed by the final adjudication
of such issue.


<PAGE>


                                   SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in Radnor, Commonwealth of Pennsylvania, on December 26, 2006.

                                       PolyMedix, Inc.

                                       By: /s/ Nicholas Landekic
                                       ----------------------------------------
                                       Nicholas Landekic
                                       President and Chief Executive Officer


                                POWER OF ATTORNEY

       Each person whose signature appears below hereby constitutes and appoints
Nicholas Landekic and Edward F. Smith his true and lawful attorney-in-fact and
agent, with full power of substitution and resubstitution for him in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this registration statement, and to file the same, with exhibits thereto and
other documents in connection therewith with the Securities and Exchange
Commission, granting unto such attorney-in-fact and agent full power and
authority to do and perform each and every act and thing requisite and necessary
in connection with such matters and hereby ratifying and confirming all that
such attorney-in-fact and agent or his substitutes may do or cause to be done by
virtue hereof.

       Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities indicated on December 26, 2006:

         Signature                                      Title

                                         President and Chief Executive Officer
/s/ Nicholas Landekic                    and Director(Principal
---------------------------------------- Executive Officer)
Nicholas Landekic

                                         Vice President, Chief Financial Officer
/s/ Edward F. Smith                      and Secretary (Principal Financial and
----------------------------------------  Accounting Officer)
Edward F. Smith

/s/ Frank P. Slattery, Jr.               Chairman of the Board of Directors
----------------------------------------
Frank P. Slattery, Jr.

/s/ Frank M. DeLape                      Director
----------------------------------------
Frank M. DeLape

/s/ William N. Kelley, M.D.              Director
----------------------------------------
William N. Kelley, M.D.

/s/ Michael E. Lewis, Ph.D               Director
----------------------------------------
Michael E. Lewis, Ph.D.

/s/ I. Wistar Morris, III                Director
----------------------------------------
I. Wistar Morris, III

/s/ Shaun F. O'Malley                    Director
----------------------------------------
Shaun F. O'Malley


<PAGE>


                                  EXHIBIT INDEX

Exhibits

   4.1     PolyMedix, Inc. 2005 Omnibus Equity Compensation Plan.

   4.2     PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan.

   5.1     Opinion of Pepper Hamilton LLP as to the validity of the securities
           being registered.

   23.1    Consent of Deloitte & Touche LLP.

   23.2    Consent of Pepper Hamilton LLP (included in Exhibit 5.1 hereto).

   24.1    Powers of Attorney (included on the signature page hereto).
[{"type": "S-8", "sequence": "1", "filename": "s-8.txt", "description": "S-8.TXT", "secsgml_size_bytes": 22604}]
{"company-data": {"conformed-name": "POLYMEDIX INC", "cik": "0001341843", "assigned-sic": "2834", "irs-number": "000000000"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-139686", "film-number": "061299750"}, "business-address": {"street1": "C/O POLYMEDIX INC", "street2": "3701 MARKET STREET STE 442", "city": "PHILADELPHIA", "state": "PA", "zip": "19104", "phone": "2159666199"}, "mail-address": {"street1": "C/O POLYMEDIX INC", "street2": "3701 MARKET STREET STE 442", "city": "PHILADELPHIA", "state": "PA", "zip": "19104"}, "former-company": {"former-conformed-name": "BTHC II ACQUISITION CORP", "date-changed": "20051019"}}
As filed with the Securities and Exchange Commission on December 26, 2006

================================================================================

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                 ---------------

                                    FORM S-8
             REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933
                                 ---------------

                                 PolyMedix, Inc.
             (Exact Name of Registrant as Specified in Its Charter)
                               Delaware 27-0125925
      (State or Other Jurisdiction (I.R.S. Employer Identification Number)
                         of Incorporation or Operation)
                      170 N. Radnor-Chester Road, Suite 300
                           Radnor, Pennsylvania 19087
          (Address of Principal Executive Offices, including Zip Code)
                   ------------------------------------------
              PolyMedix, Inc. 2005 Omnibus Equity Compensation Plan
          PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan
                            (Full Title of the Plan)
                   -------------------------------------------
                                Nicholas Landekic
                      President and Chief Executive Officer
                      170 N. Radnor-Chester Road, Suite 300
                           Radnor, Pennsylvania 19087
                                 (484) 598-2400
 (Name, Address And Telephone Number, Including Area Code, of Agent For Service)
                 ----------------------------------------------
                          Copies of communications to:
                                Jeffrey P. Libson
                               Pepper Hamilton LLP
                                 400 Berwyn Park
                                899 Cassatt Road
                                Berwyn, PA 19312
                                 (610) 640-7800
                 ----------------------------------------------
                         CALCULATION OF REGISTRATION FEE
=====================================================================================================================
                                                   Proposed maximum        Proposed maximum
     Title of shares to be       Amount to be     offering price per      aggregate offering         Amount of
          registered            registered (1)          share                   price             registration fee
---------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par value)    1,116,000(2)          $3.25(3)             $3,627,000                   $389
---------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par value)    2,884,000(4)          $1.50(3)             $4,326,000                   $463
---------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par value)    1,423,000(5)          $1.50(3)             $2,134,500                   $229
=====================================================================================================================
--------------------------------------------------------------------------------
(1) Pursuant to Rule 416(b), there shall also be deemed covered hereby any
additional securities that may hereinafter be offered or issued to prevent
dilution resulting from stock splits, stock dividends, recapitalizations or
certain other capital adjustments.

(2) Consists of shares issuable under the PolyMedix, Inc. 2005 Omnibus Equity
Compensation Plan.

(3) Estimated solely for the purposes of calculating the registration fee in
accordance with Rule 457(h)(1) and (c) under the Securities Act of 1933. As to
shares subject to outstanding but unexercised options, the price and fee are
computed based upon the weighted average exercise price of $1.50 per share. As
to the 30,000 shares issued pursuant to grants of common stock pursuant to the
2005 Omnibus Equity Compensation Plan, the price and fee are based on the value
per share on the date of grant, which was $1.50 in all cases. As to the
remaining shares, the price and fee are computed based upon $3.25 per share, the
average of the high and low prices for the common stock reported on the
Over-the-Counter Bulletin Board on December 21, 2006.
(4) Consists of shares purchasable upon exercise of options outstanding to
purchase common stock as well as grants of common stock issued and outstanding,
both as of the date hereof, under the 2005 Omnibus Equity Compensation Plan. The
amount of shares issuable pursuant to such options may again become available
for grant and issuance in the event the outstanding options expire or are
forfeited prior to being exercised.

(5) Consists of shares purchasable upon exercise of options outstanding to
purchase common stock under the 2002 Equity Compensation Plan.
PART I
              INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

Item 1.  Plan Information.

       The document(s) containing the information specified in Part I of Form
S-8 will be sent or given to participants in the Plans as specified by Rule
428(b)(1) of the Securities Act of 1933, as amended (the "Securities Act"). Such
documents are not being filed with the Securities and Exchange Commission (the
"Commission"), but constitute, along with the documents incorporated by
reference into this Registration Statement, a prospectus that meets the
requirements of Section 10(a) of the Securities Act.

Item 2.  Registrant Information and Employee Plan Annual Information.

       PolyMedix, Inc. (the "Registrant" or "Small Business Issuer") will
furnish without charge to each person to whom the prospectus is delivered, upon
the written or oral request of such person, a copy of any and all of the
documents incorporated by reference, other than exhibits to such documents
(unless such exhibits are specifically incorporated by reference to the
information that is incorporated). Requests should be directed to PolyMedix,
Inc., 170 N. Radnor Chester Road, Suite 300, Radnor, Pennsylvania 19087,
Attention: Edward F. Smith, Vice President, Chief Financial Officer and
Secretary; telephone number (484) 598-2332.

                                     PART II
               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  Incorporation of Documents by Reference.

         The following documents which have been filed by the Registrant with
the Commission are incorporated by reference into this Registration Statement:

         (a) The Registrant's Annual Registration Statement on Form 10-SB
(Registration No. 333-51895) filed with the Commission on April 5, 2006 (as
amended by Amendment No. 1 filed with the Commission on May 24, 2006 and
Amendment No. 2 filed with the Commission on June 19, 2006 and collectively, the
"Registration Statement on Form 10-SB"); Quarterly Report on Form 10-QSB for the
quarter ended June 30, 2006 filed with the Commission on August 14, 2006;
Quarterly Report on Form 10-QSB for the quarter ended September 30, 2006 filed
with the Commission on November 13, 2006; Current Report on Form 8-K filed with
the Commission on August 1, 2006; Current Report on Form 8-K filed with the
Commission on November 13, 2006; Current Report on Form 8-K filed with the
Commission on November 15, 2006; and Current Report on December 20, 2006.

         (b) The description of the Registrant's Common Stock contained in the
Registrant's Registration Statement on Form 10-SB filed, including any
amendments or reports filed for the purpose of updating such description in
which there is described the terms, rights and provisions applicable to the
Registrant's Common Stock.

         All documents filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), after the date hereof and prior to the filing of a
post-effective amendment which indicates that all securities offered pursuant to
this Registration Statement have been sold or which deregisters all securities
then remaining unsold shall be deemed to be incorporated by reference herein and
to be a part hereof from the date of filing of such documents.

Item 4.  Description of Securities.

         Not applicable.
Item 5.  Interests of Named Experts and Counsel.

         Not applicable.

Item 6.  Indemnification of Directors and Officers.

       Section 102 of the General Corporation Law of the State of Delaware
permits a corporation to eliminate the personal liability of directors of a
corporation to the corporation or its stockholders for monetary damages for a
breach of fiduciary duty as a director, except where the director breached his
duty of loyalty, failed to act in good faith, engaged in intentional misconduct
or knowingly violated a law, authorized the payment of a dividend or approved a
stock repurchase in violation of Delaware corporate law or obtained an improper
personal benefit. The Registrant's Amended and Restated Certificate of
Incorporation, as amended, provides that a director of the Registrant shall not
be personally liable to it or its stockholders for monetary damages for any
breach of fiduciary duty as a director, except to the extent that such exemption
from liability or limitation thereof is not permitted under the General
Corporation Law of the State of Delaware as currently in effect or as the same
may hereafter be amended.

       Section 145 of the General Corporation Law of the State of Delaware
provides that a corporation has the power to indemnify a director, officer,
employee, or agent of the corporation and other persons serving at the request
of the corporation in related capacities against expenses (including attorneys'
fees), judgments, fines and amounts paid in settlements actually and reasonably
incurred by the person in connection with an action, suit or proceeding to which
he is or is threatened to be made a party by reason of such position, if such
person acted in good faith and in a manner he reasonably believed to be in or
not opposed to the best interests of the corporation, and, in any criminal
action or proceeding, had no reasonable cause to believe his conduct was
unlawful, except that, in the case of actions brought by or in the right of the
corporation, no indemnification shall be made with respect to any claim, issue
or matter as to which such person shall have been adjudged to be liable to the
corporation unless and only to the extent that the Court of Chancery or other
adjudicating court determines that, despite the adjudication of liability but in
view of all of the circumstances of the case, such person is fairly and
reasonably entitled to indemnify for such expenses which the Court of Chancery
or such other court shall deem proper.

       The Registrant's Amended and Restated Certificate of Incorporation
provides that the Registrant will indemnify and advance expenses upon request to
any person who is or was a party or threatened to be made a party to any
threatened, pending or completed action, suit, proceeding or claim, whether
civil, criminal, administrative or investigative, by reason of the fact that he
or she is or was or has agreed to become, a director, officer or employee of the
Registrant or, at the election of the Registrant's board of directors, an agent
of the Registrant or is or was serving at the request of the Registrant as a
director, officer or employee or, at the election of the Registrant's board or
directors, agent of any other corporation, partnership, joint venture, trust or
other enterprise against any and all expenses (including attorneys' fees),
judgments, fines, penalties and amounts paid in settlement or incurred in
connection with the investigation, preparation to defend or defense or such
action, suit, proceeding or claim.

       The Registrant has purchased certain liability insurance for its officers
and directors.

Item 7.  Exemption From Registration Claimed.

         Not applicable.

Item 8.  Exhibits.

         4.1      PolyMedix, 2005 Omnibus Equity Compensation Plan.

         4.2      PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan.

         5.1      Opinion of Pepper Hamilton LLP as to the validity of the
                  securities being registered.

         23.1     Consent of Deloitte & Touche LLP.
23.2     Consent of Pepper Hamilton LLP (included in Exhibit 5.1
                  hereto).

         24.1     Powers of Attorney (included on the signature page hereto).

Item 9.  Undertakings.

         (a) The undersigned Small Business Issuer hereby undertakes, pursuant
to Item 512 of Regulation S-B:

                  (1) To file, during any period in which offers or sales are
                  being made, a post-effective amendment to this Registration
                  Statement:

                  (i)   To include any prospectus required by Section 10(a)(3)
                        of the Securities Act of 1933.

                  (ii)  To reflect in the prospectus any facts or events which,
                        individually or together, represent a fundamental change
                        in the information in the Registration Statement.
                        Notwithstanding the foregoing, any increase or decrease
                        in volume of securities offered (if the total dollar
                        value of securities offered would not exceed that which
                        was registered) and any deviation from the low or high
                        end of the estimated maximum offering range may be
                        reflected in the form of prospectus filed with the
                        Securities and Exchange Commission pursuant to Rule
                        424(b) if, in the aggregate, the changes in volume and
                        price represent no more than a 20% change in the maximum
                        aggregate offering price set forth in the "Calculation
                        of Registration Fee" table in the effective Registration
                        Statement.

                  (iii) To  include   any   additional   or   changed   material
                        information on the plan of distribution.

                        Provided, however, that paragraphs (a)(1)(i) and (a)(1)
                        (ii) do not apply if the information required to be
                        included in a post-effective amendment by those
                        paragraphs is contained in periodic reports filed by the
                        Registrant pursuant to Section 13 or Section 15(d) of
                        the Securities Exchange Act of 1934 that are
                        incorporated by reference in the Registration Statement.

                  (2) For determining any liability under the Securities Act of
                  1933, treat each such post-effective amendment as a new
                  registration statement of the securities offered, and the
                  offering of the securities at that time shall be deemed to be
                  the initial bona fide offering.

                  (3) File a post-effective amendment to remove from
                  registration any of the securities being registered that
                  remain unsold at the end of the offering.

                  (4) For determining liability of the undersigned Small
                  Business Issuer under the Securities Act to any purchaser in
                  the initial distribution of securities, the undersigned Small
                  Business Issuer undertakes that in a primary offering of
                  securities of the undersigned Small Business Issuer pursuant
                  to this Registration Statement, regardless of the underwriting
                  method used to sell the securities to the purchaser, if the
                  securities are offered or sold to such purchaser by means of
                  any of the following communications, the undersigned Small
                  Business Issuer will be a seller to the purchaser and will be
                  considered to offer or sell such securities to such purchaser:

                  (i)   Any preliminary prospectus or prospectus of the
                        undersigned Small Business Issuer relating to the
                        offering required to be filed pursuant to Rule 424;

                  (ii)  Any free writing prospectus relating to the offering
                        prepared by or on behalf of the undersigned Small
                        Business Issuer or used or referred to by the
                        undersigned Small Business Issuer;
(iii) The portion of any other free writing prospectus
                        relating to the offering containing material information
                        about the undersigned Small Business Issuer or its
                        securities provided by or on behalf of the undersigned
                        Small Business Issuer; and

                  (iv)  Any other communication that is an offer in the offering
                        made by the undersigned Small Business Issuer to the
                        purchaser.

         (e) Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the Small
Business Issuer has been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Securities Act and is, therefore, unenforceable. In the event that a
claim for indemnification against such liabilities (other than the payment by
the registrant of expenses incurred or paid by a director, officer or
controlling person of the registrant in the successful defense of any action,
suit or proceeding) is asserted by such director, officer or controlling person
in connection with the securities being registered, the Small Business Issuer
will, unless in the opinion of its counsel the matter has been settled by
controlling precedent, submit to a court of appropriate jurisdiction the
question whether such indemnification by it is against public policy as
expressed in the Securities Act and will be governed by the final adjudication
of such issue.
SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in Radnor, Commonwealth of Pennsylvania, on December 26, 2006.

                                       PolyMedix, Inc.

                                       By: /s/ Nicholas Landekic
                                       ----------------------------------------
                                       Nicholas Landekic
                                       President and Chief Executive Officer

                                POWER OF ATTORNEY

       Each person whose signature appears below hereby constitutes and appoints
Nicholas Landekic and Edward F. Smith his true and lawful attorney-in-fact and
agent, with full power of substitution and resubstitution for him in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this registration statement, and to file the same, with exhibits thereto and
other documents in connection therewith with the Securities and Exchange
Commission, granting unto such attorney-in-fact and agent full power and
authority to do and perform each and every act and thing requisite and necessary
in connection with such matters and hereby ratifying and confirming all that
such attorney-in-fact and agent or his substitutes may do or cause to be done by
virtue hereof.

       Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities indicated on December 26, 2006:

         Signature                                      Title

                                         President and Chief Executive Officer
/s/ Nicholas Landekic                    and Director(Principal
---------------------------------------- Executive Officer)
Nicholas Landekic

                                         Vice President, Chief Financial Officer
/s/ Edward F. Smith                      and Secretary (Principal Financial and
----------------------------------------  Accounting Officer)
Edward F. Smith

/s/ Frank P. Slattery, Jr.               Chairman of the Board of Directors
----------------------------------------
Frank P. Slattery, Jr.

/s/ Frank M. DeLape                      Director
----------------------------------------
Frank M. DeLape

/s/ William N. Kelley, M.D.              Director
----------------------------------------
William N. Kelley, M.D.

/s/ Michael E. Lewis, Ph.D               Director
----------------------------------------
Michael E. Lewis, Ph.D.

/s/ I. Wistar Morris, III                Director
----------------------------------------
I. Wistar Morris, III

/s/ Shaun F. O'Malley                    Director
----------------------------------------
Shaun F. O'Malley
EXHIBIT INDEX

Exhibits

   4.1     PolyMedix, Inc. 2005 Omnibus Equity Compensation Plan.

   4.2     PolyMedix Pharmaceuticals, Inc. 2002 Equity Compensation Plan.

   5.1     Opinion of Pepper Hamilton LLP as to the validity of the securities
           being registered.

   23.1    Consent of Deloitte & Touche LLP.

   23.2    Consent of Pepper Hamilton LLP (included in Exhibit 5.1 hereto).

   24.1    Powers of Attorney (included on the signature page hereto).