##### 



As filed with the Securities and Exchange Commission on July 12, 2006
 Registration No. 333-
   UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, DC 20549
 
 FORM S-8
 AND POST-EFFECTIVE AMENDMENT NO. 2
 AND POST-EFFECTIVE AMENDMENT NO. 1
 REGISTRATION STATEMENT
 UNDER THE SECURITIES ACT OF 1933
 
 Nastech Pharmaceutical Company Inc.
 (Exact name of registrant as specified in its charter)
 Delaware
    
    2834
    
    11-2658569(State or other jurisdiction of
    
    (Primary Standard Industrial
    
    (I.R.S. Employerincorporation or organization)
    
    Classification Code Number)
    
    Identification Number)
 3450 Monte Villa Parkway
Bothell, Washington 98021
(425) 908-3600  (Address of Principal Executive Offices)
 NASTECH PHARMACEUTICAL COMPANY INC.
2004 STOCK INCENTIVE PLAN  (Full Title of the Plan)
 Dr. Steven C. Quay
Chairman, President and Chief Executive Officer
Nastech Pharmaceutical Company Inc.
3450 Monte Villa Parkway
Bothell, Washington 98021  (Name and Address of Agent for Service)
 (425) 908-3600  (Telephone Number, Including Area Code, of Agent for
Service)  Copies to:
 Blake Hornick, Esq.
Pryor Cashman Sherman & Flynn LLP
410 Park Avenue
New York, New York 10022
(212) 326-0133
 CALCULATION OF REGISTRATION FEE
 Proposed Maximum
    
    
    Proposed MaximumTitle of Securities
    
    
    Amount to be
    
    
    Offering Price Per
    
    
    Aggregate Offering
    
    
    Amount ofto be Registered
    
    
    Registered(1)
    
    
    Security(2)
    
    
    Price(2)
    
    
    Registration Fee(2)Nastech Pharmaceutical Company Inc.
2004 Stock Incentive Plan
Common Stock ($0.006 par value)
    
    
    2,350,000(3)
    
    
    $15.43(4)
    
    
    $36,260,500(4)
    
    
    $3,879.87(5)
 (1)
    
    Pursuant to Rule 416(a) under the Securities Act of 1933, as amended (the Securities Act),
this Registration Statement shall also cover any additional shares of Nastech Pharmaceutical
Company Inc. (the Company) common stock, par value $0.006 per share (the Common Stock),
which become issuable under the Nastech Pharmaceutical Company Inc. 2004 Stock Incentive Plan
(the Plan) by reason of any stock dividend, stock split, recapitalization or other similar
transaction effected without the receipt of consideration which results in an increase in the
number of the outstanding shares of common stock of Nastech Pharmaceutical Company Inc.(2)
    
    In U.S. dollars or the equivalent thereof denominated in one or more foreign currencies or
units of two or more foreign currencies or composite currencies. Estimated solely for the
purposes of calculating the registration fee.(3)
    
    Pursuant to Rule 429(b) under the Securities Act, the 2,350,000 shares of Common Stock being
registered hereunder includes: (i) 600,000 shares of Common Stock issuable pursuant to the
Plan that were previously registered on a registration statement on Form S-8 (File No.
333-118206) filed by the Company with the Securities and Exchange Commission (the SEC) on
August 13, 2004 (the 2004 Registration Statement), and (ii) 750,000 shares of Common Stock
issuable pursuant to the Plan that were previously registered on a registration statement on
Form S-8 (File No. 333-126905) filed by the Company with the SEC on July 27, 2005 (the 2005
Registration Statement). Accordingly, this registration statement also constitutes
post-effective amendment no. 2 to the 2004 Registration Statement and post-effective amendment
no. 1 to the 2005 Registration Statement.(4)
    
    Calculated in accordance with Rule 457(c) of the Securities Act, solely for the purpose of
calculating the registration fee on the basis of the average of the high and low prices of our
Common Stock as reported by The Nasdaq National Market on July 5, 2006.(5)
    
    Pursuant to General Instruction E of Form S-8, a registration fee of $1,651.01 is being paid
with respect to the 1,000,000 additional shares of Common Stock being registered on this
Registration Statement, calculated in accordance with Rule 457(o) under the Securities Act at
the statutory rate of $107.00 per $1,000,000 of securities registered. A registration fee of
$660.61 was previously paid on August 13, 2004 in connection with the filing of the 2004
Registration Statement relating to 600,000 shares under the Plan and a registration fee of
$1,227.03 was previously paid on July 26, 2005 in connection with the filing of the 2005
Registration Statement relating to 750,000 shares under the Plan.




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Explanatory Notes




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PROSPECTUS
 Nastech Pharmaceutical Company Inc.
 1,067,814 shares of
Common Stock
     
 You should carefully read and consider the risk factors beginning on page 25 in our Annual
Report on Form 10-K for the year ended December 31, 2005 for risks relating to investments in our
securities.
 
 
 
 Neither the Securities and Exchange Commission nor any state securities commission has approved or
disapproved of these securities or determined if this prospectus is truthful or complete. Any
representation to the contrary is a criminal offense.




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TABLE OF CONTENTS
 Information About The Company
    
    
    1Forward-Looking Statements
    
    
    4Use of Proceeds
    
    
    5Selling Stockholders
    
    
    6Plan of Distribution
    
    
    10Description of Common Stock
    
    
    12Legal Matters
    
    
    13Experts
    
    
    13Where You Can Find More Information
    
    
    14
   i




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Unless the context otherwise requires, all references in this prospectus to Nastech, Company,
registrant, we, us or our include Nastech Pharmaceutical Company Inc., a Delaware
corporation, and any subsidiaries or other entities controlled by us. All references in this
prospectus to common stock refer to our common stock, par value $0.006 per share.
 INFORMATION ABOUT THE COMPANY
 Overview
     Employees
  1




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Liability and Indemnification of Directors and Officers
     2




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Corporate Information
 http://www.nastech.com
 3




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FORWARD-LOOKING STATEMENTS
    
    
    our ability to obtain additional funding;
    
    our efforts to establish and maintain collaboration partnerships for the development
of PTH(1-34) intranasal spray, PYY intranasal spray, generic calcitonin-salmon intranasal
spray, morphine gluconate intranasal spray, insulin, RNA interference or other programs;
    
    the success or failure of our research and development programs or the programs of our partners;
    
    the advantages and disadvantages of pharmaceuticals delivered intranasally;
    
    the need for improved and alternative drug delivery methods;
    
    our efforts to collaborate with other pharmaceutical and biotechnology companies that
have products under development;
    
    our ability to successfully complete product research and development, including
pre-clinical and clinical studies and commercialization;
 4




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
    
    our ability to obtain governmental approvals, including product and patent approvals;
    
    our ability to successfully manufacture the products of our research and development
programs and our marketed products to meet current good manufacturing practices and to
manufacture these products at a financially acceptable cost;
    
    our ability to attract and retain our key officers and employees and manufacturing,
sales, distribution and marketing partners;
    
    costs associated with any product liability claims, patent prosecution, patent
infringement lawsuits and other lawsuits;
    
    our ability to develop and commercialize our products before our competitors; and
    
    the projected size of the drug delivery market.
   USE OF PROCEEDS
  5




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SELLING STOCKHOLDERS
   Number of
    
    Number of
    
    Number ofShares Owned
    
    Shares
    
    Shares to BePrior to
    
    Registered
    
    Owned AfterName and Position With Us
    
    Offering(1)
    
    Hereby(2)
    
    Offering(3)Steven C. Quay, M.D., Ph.D.
    
    
    2,002,575
    
    
    
    768,000
    
    
    
    1,234,575Chairman of the Board, President and
Chief Executive OfficerDr. Gordon C. Brandt
    
    
    132,500
    
    
    
    12,500
    
    
    
    120,000Executive Vice President Clinical Research and
Medical AffairsDr. Paul H. Johnson
    
    
    112,565
    
    
    
    11,065
    
    
    
    101,500Senior Vice President, Research and
Development and Chief Scientific OfficerPhilip C. Ranker
    
    
    73,233
    
    
    
    58,233
    
    
    
    15,000Chief Financial Officer and SecretaryDavid E. Wormuth
    
    
    55,833
    
    
    
    5,000
    
    
    
    50,833Senior Vice President, OperationsTimothy M. Duffy
    
    
    67,592
    
    
    
    33,592
    
    
    
    34,000Executive Vice President, Marketing and
Business
DevelopmentBruce R. York
    
    
    13,749
    
    
    
    11,749
    
    
    
    2,000Chief Accounting Officer and Assistant SecretarySusan B. Bayh
    
    
    43,235
    
    
    
    20,235
    
    
    
    23,000Director
 6




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Number of
    
    Number of
    
    Number ofShares Owned
    
    Shares
    
    Shares to BePrior to
    
    Registered
    
    Owned AfterName and Position With Us
    
    Offering(1)
    
    Hereby(2)
    
    Offering(3)J. Carter Beese, Jr.
    
    
    85,000
    
    
    
    12,500
    
    
    
    72,500DirectorDr. Alexander D. Cross, Ph.D.
    
    
    49,000
    
    
    
    21,500
    
    
    
    27,500DirectorDr. Ian R. Ferrier
    
    
    29,235
    
    
    
    9,235
    
    
    
    20,000DirectorMyron Z. Holubiak
    
    
    51,235
    
    
    
    23,735
    
    
    
    27,500DirectorLeslie D. Michelson
    
    
    74,470
    
    
    
    27,970
    
    
    
    46,500DirectorJohn V. Pollock
    
    
    98,333
    
    
    
    12,500
    
    
    
    85,833DirectorGerald T. Stanewick
    
    
    178,712
    
    
    
    20,000
    
    
    
    158,712DirectorBruce R. Thaw
    
    
    209,041
    
    
    
    11,000
    
    
    
    194,041DirectorDevin N. Wenig
    
    
    387,953
    
    
    
    9,000
    
    
    
    378,953DirectorTOTAL:
    
    
    3,664,261
    
    
    
    1,067,814
    
    
    
    2,592,447
 
 (1)
    
    Includes shares of Common Stock acquired not pursuant to any employee or director benefit
plan, Common Stock underlying options and restricted stock granted pursuant to our 2004 Stock
Incentive Plan (both vested and unvested), Common Stock underlying options granted pursuant to
any other employee or director benefit plan (both vested and unvested), including all such
shares, options and warrants directly or indirectly held by each such Selling Stockholder.(2)
    
    Includes all common stock underlying options granted and outstanding as of June 30, 2006
(both vested and unvested), and all restricted stock issued, pursuant to our 2004 Stock
Incentive Plan.(3)
    
    Assumes all shares registered under this prospectus will be sold. 7




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PercentageName
    
    OwnershipDr. Steven C. Quay
    
    
    8.4
    %Devin N. Wenig
    
    
    1.7
    %
  Dr. Steven C. Quay.
 Dr. Gordon C. Brandt.
 Dr. Paul H. Johnson.
 Philip C. Ranker
 David E. Wormuth.
 Timothy M. Duffy.
 Bruce R. York
 8




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Susan B. Bayh.
 J. Carter Beese, Jr.
 Dr. Alexander D. Cross.
 Dr. Ian R. Ferrier.
 Myron Z. Holubiak.
 Leslie D. Michelson.
 John V. Pollock.
 Gerald T. Stanewick.
 Bruce R. Thaw.
 Devin N. Wenig.
 9




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PLAN OF DISTRIBUTION
  
    
    our Common Stock may be sold through a broker or brokers, acting as principals or
agents. Transactions through broker-dealers may include block trades in which
brokers or dealers will attempt to sell our Common Stock as agent but may position
and resell the block as principal to facilitate the transaction. Our Common Stock
may be sold through dealers or agents or to dealers acting as market makers.
Broker-dealers may receive compensation in the form of discounts, concessions, or
commissions from the selling stockholders and/or the purchase of our Common Stock
for whom such broker-dealers may act as agents or to whom they sell as principal, or
both (which compensation as to a particular broker-dealer might be in excess of
customary commissions);
    
    our Common Stock may be sold on any national securities exchange or quotation
service on which our Common Stock may be listed or quoted at the time of sale, in
the over-the-counter market, or in transactions otherwise than on such exchanges or
services or in the over-the-counter market; or
    
    our Common Stock may be sold in private sales directly to purchasers.
    10




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
    
    the name of each such Selling Stockholder and of the participating broker-dealer(s);
    
    the number of shares involved;
    
    the price at which such shares were sold;
    
    the commissions paid or discounts or concessions allowed to such
broker-dealer(s), where applicable;
    
    that such broker-dealer(s) did not conduct any investigation to verify the
information set out or incorporated by reference in this prospectus; and
    
    other facts material to the transaction.
  11




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DESCRIPTION OF COMMON STOCK
  General
   Stockholder Rights Plan
  12
      Transfer Agent
  LEGAL MATTERS
  EXPERTS
  13
      WHERE YOU CAN FIND MORE INFORMATION
 http://www.sec.gov. http://www.nastech.com.
  14
      You should rely only on the information contained in or incorporated by reference into this
prospectus. We have not authorized any person to give any information or to make any
representations other than those contained or incorporated by reference in this prospectus, and, if
given or made, you must not rely upon such information or representations as having been
authorized. This prospectus does not constitute an offer to sell or the solicitation of an offer to
buy any securities other than the securities described in this prospectus or an offer to sell or
the solicitation to buy such securities in any circumstances in which such offer or solicitation is
unlawful. You should not assume that the information we have included in this prospectus is
accurate as of any date other than the date of this prospectus or that any information we have
incorporated by reference is accurate as of any date other than the date of the document
incorporated by reference regardless of the time of delivery of this prospectus or of any
securities registered hereunder.
 
 
 
 1,067,814 Shares
 Nastech Pharmaceutical Company Inc.
 Common Stock
 
 PROSPECTUS
 
 July 12, 2006
      PART II
 INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
 Item 3. Incorporation of Documents by Reference.
          Item 4. Description of Securities.
      Item 5. Interests of Named Experts and Counsel.
  Item 6. Indemnification of Directors and Officers.
      Item 7. Exemption from Registration Claimed.
  Item 8. Exhibits.
 ExhibitNo.
    
    Description4.1
    
    Form of Common Stock Certificate (filed as Exhibit 4.1 to our Registration
Statement on Form S-3, File No. 333-119429, and incorporated herein by
reference).4.2
    
    Rights Agreement, dated February 22, 2000, between the Company and
American Stock Transfer & Trust Company as Rights Agent (filed as Exhibit
1 to our Current Report on Form 8-K dated February 22, 2000 and
incorporated herein by reference).5.1
    
    Opinion of Pryor Cashman Sherman & Flynn LLP. (1)10.1
    
    Nastech Pharmaceutical Company Inc. 2004 Stock Incentive Plan (filed as
Exhibit 99 to our Registration Statement on Form S-8, File No. 333-118206,
and incorporated herein by reference).10.2
    
    Amendment No. 1 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan dated July 20, 2005 (filed as Exhibit 10.4 to our Current
Report on Form 8-K dated July 20, 2005, and incorporated herein by
reference).10.3
    
    Amendment No. 2 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan (filed as Exhibit 10.18 to the Companys Quarterly Report
on Form 10-Q for the Quarter Ended September 30, 2005 and incorporated
herein by reference).10.4
    
    Amendment No. 3 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan. (filed as Exhibit 10.24 to the Companys Annual Report on
Form 10-K for the year ended December 31, 2005 and incorporated herein by
reference).10.5
    
    Amendment No. 4 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan dated June 13, 2006. (1)23.1
    
    Consent of KPMG LLP, independent registered public accounting firm. (1)23.2
    
    Consent of Pryor Cashman Sherman & Flynn LLP (included in Exhibit 5.1). (1)24.1
    
    Power of Attorney (included on the signature page). (1)
      (1)
    
    Filed herewith. Item 9. Undertakings
      
      SIGNATURES
 th
 NASTECH PHARMACEUTICAL COMPANY INC.By:
    /s/ Steven C. QuaySteven C. Quay, M.D., Ph.D.Chairman of the Board, President
and
Chief Executive Officer   Signature
    
    Title
    
    Date/s/ Steven C. Quay

Steven C. Quay, M.D., Ph.D.
    
    Chairman of the Board, President and
Chief Executive Officer
(Principal Executive Officer)
    
    July 12, 2006/s/ Philip C. Ranker

Philip C. Ranker
    
    Chief Financial Officer
(Principal Financial Officer)
    
    July 12, 2006/s/ Bruce R. York

Bruce R. York
    
    Chief Accounting Officer
(Principal Accounting Officer)
    
    July 12, 2006/s/ Susan B. Bayh

Susan B. Bayh
    
    Director
    
    July 12, 2006/s/ J. Carter Beese, Jr.

J. Carter Beese, Jr.
    
    Director
    
    July 12, 2006/s/ Alexander D. Cross

Dr. Alexander D. Cross
    
    Director
    
    July 12, 2006
      Signature
    
    Title
    
    Date/s/ Ian R. Ferrier

Dr. Ian R. Ferrier
    
    Director
    
    July 12, 2006/s/ Myron Z. Holubiak

Myron Z. Holubiak
    
    Director
    
    July 12, 2006/s/ Leslie D. Michelson

Leslie D. Michelson
    
    Director
    
    July 12, 2006/s/ John V. Pollock

John V. Pollock
    
    Director
    
    July 12, 2006/s/ Gerald T. Stanewick

Gerald T. Stanewick
    
    Director
    
    July 12, 2006/s/ Bruce R. Thaw

Bruce R. Thaw
    
    Director
    
    July 12, 2006/s/ Devin N. Wenig

Devin N. Wenig
    
    Director
    
    July 12, 2006
      EXHIBIT INDEX
 ExhibitNo.
    
    Description4.1
    
    Form of Common Stock Certificate (filed as Exhibit 4.1 to our Registration
Statement on Form S-3, File No. 333-119429, and incorporated herein by
reference).4.2
    
    Rights Agreement, dated February 22, 2000, between the Company and
American Stock Transfer & Trust Company as Rights Agent (filed as Exhibit
1 to our Current Report on Form 8-K dated February 22, 2000 and
incorporated herein by reference).5.1
    
    Opinion of Pryor Cashman Sherman & Flynn LLP. (1)10.1
    
    Nastech Pharmaceutical Company Inc. 2004 Stock Incentive Plan (filed as
Exhibit 99 to our Registration Statement on Form S-8, File No. 333-118206,
and incorporated herein by reference).10.2
    
    Amendment No. 1 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan dated July 20, 2005 (filed as Exhibit 10.4 to our Current
Report on Form 8-K dated July 20, 2005, and incorporated herein by
reference).10.3
    
    Amendment No. 2 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan (filed as Exhibit 10.18 to the Companys Quarterly Report
on Form 10-Q for the Quarter Ended September 30, 2005 and incorporated
herein by reference).10.4
    
    Amendment No. 3 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan. (filed as Exhibit 10.24 to the Companys Annual Report on
Form 10-K for the year ended December 31, 2005 and incorporated herein by
reference).10.5
    
    Amendment No. 4 to Nastech Pharmaceutical Company Inc. 2004 Stock
Incentive Plan dated June 13, 2006. (1)23.1
    
    Consent of KPMG LLP, independent registered public accounting firm. (1)23.2
    
    Consent of Pryor Cashman Sherman & Flynn LLP (included in Exhibit 5.1). (1)24.1
    
    Power of Attorney (included on the signature page). (1)
 
 (1)
    
    Filed herewith.