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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549
 
 FORM 10-Q x
    
    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934
 For the Quarter Ended March 31, 2004 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934
 For the Period from _____ to _____ Commission File Number 0-21481 TRANSKARYOTIC THERAPIES, INC.  Delaware
(State or other jurisdiction of
incorporation or organization)
    
    04-3027191
(I.R.S. Employer
Identification No.)
 700 Main Street
Cambridge, Massachusetts
(Address of principal executive offices)
    
    02139
(Zip Code)
 Registrants telephone number, including area code: (617) 349-0200   Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes   
x    No    o Indicate by check mark whether the registrant is an accelerated filer (as
defined in Rule 12b-2 of the Securities Exchange Act of 1934, as amended). Yes   
x    No    o At April 30, 2004, there were 34,627,654 shares of Common Stock, $.01 par
value, outstanding.




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Transkaryotic Therapies, Inc.  
 INDEX PART I. FINANCIAL INFORMATIONItem 1. Condensed Consolidated Financial Statements (unaudited)Condensed Consolidated Balance Sheets as of March 31, 2004 and December 31, 2003
    
    
    3Condensed Consolidated Statements of Operations for the Three Months Ended March 31, 2004 and March 31, 2003
    
    
    4Condensed Consolidated Statements of Cash Flows For the Three Months ended March 31, 2004 and March 31, 2003
    
    
    5Notes to Condensed Consolidated Financial Statements
    
    
    6Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    12Item 3. Quantitative and Qualitative Disclosures About Market Risk
    
    
    36Item 4. Controls and Procedures
    
    
    36PART II. OTHER INFORMATIONItem 1. Legal Proceedings
    
    
    37Item 6. Exhibits and Reports on Form 8-K
    
    
    37SIGNATURESEXHIBIT INDEXEx-10.42 Amended License AgreementEx-31.1 Certification of CEOEx-31.2 Certification of CFOEx-32.1 Certification of CEO pursuant to Sect 906Ex-32.2 Certification of CFO pursuant to Sect 906
  2




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PART I            FINANCIAL INFORMATION 
 Item 1. Condensed Consolidated Financial Statements Transkaryotic Therapies, Inc. 
  March 31,
    
    December 31,(in thousands, except par values)
    
    2004
    
    2003Assets
    
    (unaudited)Current assets:Cash and cash equivalents
    
    $
    156,643
    
    
    $
    172,954Marketable securities
    
    
    7,991
    
    
    
    7,993Accounts receivable
    
    
    22,838
    
    
    
    23,064Inventories
    
    
    15,180
    
    
    
    16,741Prepaid expenses and other current assets
    
    
    6,363
    
    
    
    4,587Total current assets
    
    
    209,015
    
    
    
    225,339Property and equipment, net
    
    
    64,644
    
    
    
    61,908Other assets
    
    
    1,972
    
    
    
    1,922Total assets
    
    $
    275,631
    
    
    $
    289,169Liabilities and Stockholders EquityCurrent liabilities:Accounts payable
    
    $
    8,005
    
    
    $
    7,466Accrued expenses
    
    
    14,764
    
    
    
    11,925Current portion of accrued restructuring charges
    
    
    1,472
    
    
    
    1,523Current portion of deferred revenue
    
    
    235
    
    
    
    235Total current liabilities
    
    
    24,476
    
    
    
    21,149Long-term portion of accrued restructuring charges
    
    
    6,158
    
    
    
    6,518Long-term portion of deferred revenue
    
    
    2,702
    
    
    
    2,767Minority interest
    
    
    414
    
    
    
    413Stockholders equity:Series B preferred stock, $.01 par value, 1,000 shares
authorized; no shares issued and outstanding at
March 31, 2004 and December 31, 2003, respectively
    
    
    
    
    
    
    Common stock, $.01 par value; 100,000 shares authorized;
34,989 and 34,974 shares issued, and 34,622 and 34,607 shares
outstanding, at March 31, 2004 and December 31, 2003, respectively
    
    
    350
    
    
    
    350Additional paid-in capital
    
    
    686,643
    
    
    
    686,545Accumulated deficit
    
    
    (454,819
    )
    
    
    (440,668
    )Accumulated other comprehensive income
    
    
    11,989
    
    
    
    14,377Less
treasury stock, at cost; 367 shares at March 31, 2004 and December 31, 2003
    
    
    (2,282
    )
    
    
    (2,282
    )Total stockholders equity
    
    
    241,881
    
    
    
    258,322Total liabilities and stockholders equity
    
    $
    275,631
    
    
    $
    289,169
 See accompanying Notes to Condensed Consolidated Financial Statements. 3




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Transkaryotic Therapies, Inc. 
   Three Months Ended March 31,(in thousands, except per share amounts)
    
    2004
    
    2003Revenues:Product sales
    
    $
    17,372
    
    
    $
    12,169License and research revenues
    
    
    62
    
    
    
    1417,434
    
    
    
    12,183Operating expenses:Cost of goods sold
    
    
    2,236
    
    
    
    3,501Research and development
    
    
    19,837
    
    
    
    20,982Intellectual property license expense
    
    
    
    
    
    
    1,350Selling, general and administrative
    
    
    8,958
    
    
    
    9,166Restructuring charges
    
    
    861
    
    
    
    3,60231,892
    
    
    
    38,601Loss from operations before minority interest
    
    
    (14,458
    )
    
    
    (26,418
    )Minority interest
    
    
    (1
    )
    
    
    (303
    )Loss from operations after minority interest
    
    
    (14,459
    )
    
    
    (26,721
    )Interest income
    
    
    308
    
    
    
    776Net loss
    
    $
    (14,151
    )
    
    $
    (25,945
    )Basic and diluted net loss per share
    
    $
    (0.41
    )
    
    $
    (0.75
    )Shares used to compute basic and diluted net
loss per share
    
    
    34,612
    
    
    
    34,550
 See accompanying Notes to Condensed Consolidated Financial Statements. 4




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Transkaryotic Therapies, Inc. 
   March 31,(in thousands)
    
    2004
    
    2003Operating activities:Net loss
    
    $
    (14,151
    )
    
    $
    (25,945
    )Adjustments to reconcile net loss to net
cash used for operating activities:Depreciation and amortization
    
    
    2,924
    
    
    
    3,013Minority interest
    
    
    1
    
    
    
    303Change in accrued intellectual property license expense
    
    
    
    
    
    
    (11,368
    )Changes in other operating assets and liabilities
    
    
    1,953
    
    
    
    (3,142
    )Net cash used for operating activities
    
    
    (9,273
    )
    
    
    (37,139
    )Investing activities:Proceeds from sales and maturities of marketable securities
    
    
    7,983
    
    
    
    54,288Purchases of marketable securities
    
    
    (7,983
    )
    
    
    (7,956
    )Purchases of property and equipment
    
    
    (5,660
    )
    
    
    (5,448
    )Changes in other assets and liabilities
    
    
    (50
    )
    
    
    (80
    )Net cash provided by (used for) investing activities
    
    
    (5,710
    )
    
    
    40,804Financing Activities:Issuance of common stock, net
    
    
    98
    
    
    
    Repurchase of treasury stock
    
    
    
    
    
    
    (2,282
    )Net cash provided by (used for) financing activities
    
    
    98
    
    
    
    (2,282
    )Effect of exchange rate changes on cash and cash equivalents
    
    
    (1,426
    )
    
    
    320Net increase (decrease) in cash and cash equivalents
    
    
    (16,311
    )
    
    
    1,703Cash and cash equivalents at January 1
    
    
    172,954
    
    
    
    154,604Cash and cash equivalents at March 31
    
    $
    156,643
    
    
    $
    156,307
 See accompanying Notes to Condensed Consolidated Financial Statements. 5




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Transkaryotic Therapies, Inc. 
   1. BASIS OF PRESENTATION The accompanying unaudited condensed consolidated financial statements have
been prepared in accordance with accounting principles generally accepted in
the United States for interim financial information and with the instructions
to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not
include all of the information and footnotes required by generally accepted
accounting principles in the United States for complete financial statements.
In the opinion of management, the accompanying financial statements include all
adjustments, consisting only of normal recurring adjustments, necessary for a
fair presentation of the financial position, results of operations and cash
flows for the periods presented. The results of operations for the interim
period ended March 31, 2004 are not necessarily indicative of the results that
may be expected for the year ending December 31, 2004 or for any other period. These financial statements should be read in conjunction with the audited
consolidated financial statements and notes thereto for the year ended December
31, 2003 included in the Companys Annual Report on Form 10-K as filed with the
Securities and Exchange Commission. Gene-Activated®, and TKT® are registered trademarks and Replagal is a
trademark of the Company. Dynepo is a trademark of Aventis Pharmaceuticals,
Inc. (Aventis) and Fabrazyme is a trademark of Genzyme Corporation
(Genzyme). All other trademarks, service marks or trade names referenced in
this quarterly report are the property of their respective owners. 2. NET LOSS PER SHARE The Company calculates net loss per share in accordance with Statement of
Financial Accounting Standard (SFAS) No. 128, Earnings Per Share, and related
interpretations. Basic earnings per share is computed using the weighted
average shares outstanding. Basic net loss per share was equivalent to diluted net loss per share for the
three months ended March 31, 2004 and 2003 because common equivalent shares
from convertible preferred stock and stock options have been excluded, as their
effect is antidilutive. 3. COMPREHENSIVE LOSS Comprehensive loss comprises net loss, unrealized gains and losses on
marketable securities designated as available-for-sale, and cumulative foreign
currency translation adjustments. The Company had a total comprehensive loss
of $16,539,000 and $25,336,000 for the three months ended March 31, 2004 and
2003, respectively. 4. REVENUE RECOGNITION The Company recognizes revenue from product sales in accordance with Staff
Accounting Bulletin 104 (SAB 104), Revenue Recognition, when there is
persuasive evidence that an arrangement exists, delivery has occurred, the
price is fixed or determinable, and collection is reasonably assured. The
Company determines that collection is reasonably assured in Europe and in some
other countries outside of the United States, once reimbursement agreements and
pricing arrangements are established and formalized, as these agreements
establish the relevant governmental agencys intent to pay, or once there are
legally binding purchase agreements between a hospital and the Company, or once
approval has been granted for the reimbursement of cost for individual
patients. The Company only records revenues in those countries for which one of
the conditions set forth in the previous sentence has been met. During the first quarter of 2004, the Company recorded a $481,000 reversal of
2003 price discount accrual to product sales, as the Company determined it was
no longer probable that this amount would be paid to customers. 5. INVENTORIES Inventories consist of the following: 6




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March 31,
    
    December 31,(in thousands)
    
    2004
    
    2003Raw materials
    
    $
    505
    
    
    $
    574Work in process
    
    
    8,594
    
    
    
    7,931Finished goods
    
    
    6,081
    
    
    
    8,236$
    15,180
    
    
    $
    16,741
 Inventories are stated at the lower of cost or market with cost determined
under a first-in, first-out method. Inventories are reviewed periodically for
slow-moving or obsolete status based on sales activity, both projected and
historical. 6. RESTRUCTURING CHARGES In February 2003, TKT announced a major reorganization in an effort to reduce
costs and narrow the scope of the Companys research initiatives. Under this
reorganization, TKT is focusing its research, development, and
commercialization efforts primarily on therapeutics for the treatment of rare
genetic diseases caused by protein deficiencies. The Company is seeking
collaborative partners for programs outside of its core focus, including its
Gene-Activated protein products, which are versions of proteins that would
compete with proteins currently being marketed by third parties, and for its
gene therapy programs. As a result of the restructuring, the Company recorded
charges of $12,461,000 in 2003 and $861,000 for the quarter ended March 31,
2004, in accordance with SFAS No. 146, Accounting for Costs Associated with
Exit or Disposal Activities. As part of this restructuring, TKT reduced its United States headcount by
approximately 100 positions and further reduced its headcount through
attrition. As of March 31, 2004, TKT had 325 full-time United States employees.
TKT has also consolidated four facilities as part of the restructuring. The
Companys employee-related and facility consolidation restructuring actions
were completed as of December 31, 2003. The Company will continue to
record restructuring charges related to vacated facility expenses during the remainder
of the lease terms until such facilities are sublet in accordance with SFAS No.
146, Accounting for Costs Associated with Exit or Disposal Activities. The remaining lease obligation costs are included in restructuring charges in
the statements of operations and accrued expenses on the balance sheet at March
31, 2004. The following table displays the restructuring activity and
liability balance included in accrued expenses: Balance at
December 31,
2003
    
    Charges
    
    Payments
    
    Other
    
    Balance at
March 31,2004(in thousands)Lease obligations
    
    $
    8,041
    
    
    $
    861
    
    
    $
    (1,233
    )
    
    $
    (39
    )
    
    $
    7,630Less: current portion of accrued restructuring charges
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (1,472
    )Long-term portion of accrued restructuring charges
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    $
    6,158
 7. STOCK BASED COMPENSATION The Company accounts for qualified stock option grants under the intrinsic
value method in accordance with Accounting Principles Board Opinion No. 25,
Accounting for Stock Issued to Employees(APB 25) and Financial Accounting
Standards Board (FASB) Interpretation No. 44, Accounting for Certain
Transactions Involving Stock Compensation, an Interpretation of APB No. 25, and
related interpretation, and, accordingly, recognizes no compensation expense
for the issue thereof. For certain non-qualified stock options granted, the
Company recognizes as compensation expense the excess of the fair value of the
common stock issuable upon exercise over the aggregate exercise price of such
options. The compensation is amortized over the vesting period of each option
or the recipients term of employment, if shorter. The Company has adopted the
disclosure-only provisions of SFAS No. 123, Accounting for Stock-Based
Compensation,as amended by SFAS No. 148, Accounting for Stock-Based
Compensation-Transition and Disclosure. The table below presents the net loss and basic and diluted net loss per common
share if compensation cost for the Companys stock option plans had been
determined based on the estimated fair value of awards under those plans on the
grant or purchase date: 7




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For the three months endedMarch 31,2004
    
    2003(in thousands, except per share prices)Net loss
    
    $
    (14,151
    )
    
    $
    (25,945
    )Deduct: Total stock-based employee
compensation expense determined under the fair
value based method for all awards
    
    
    (3,583
    )
    
    
    (7,066
    )Pro forma net loss
    
    $
    (17,734
    )
    
    $
    (33,011
    )Basic and diluted net loss per share- as reported
    
    $
    (0.41
    )
    
    $
    (0.75
    )Basic and diluted net loss per share- pro forma
    
    $
    (0.51
    )
    
    $
    (0.96
    )
 Fair values of awards granted under the stock option plans were estimated at
grant or purchase dates using a Black-Scholes option pricing model. The Company
uses the multiple option approach and the following assumptions: For the three months endedMarch 31,2004
    
    2003Expected life (years)
    
    
    1.5 - 7.5
    
    
    
    1.5 - 7.5Interest rate
    
    
    1.4% - 4.4
    %
    
    
    1.2% - 3.7
    %Expected volatility
    
    
    1.00
    
    
    
    0.95Weighted average fair value per share of
options granted during the period
    
    $
    7.67
    
    
    $
    3.06
 The Company has never declared or paid dividends on any of its capital stock
and does not expect to do so in the foreseeable future. The pro forma effects of expensing the estimated fair value of issued stock
options on net loss and net loss per share for the three months ended March 31,
2004 and 2003, respectively, are not necessarily representative of the effects
on reporting the results of operations for future years as options vest over
several years and the Company expects to grant options in future years. 8. LEGAL PROCEEDINGS The Company is a party to a number of legal proceedings. The costs related to
these proceedings have been significant and the Company expects that these
costs will continue to be significant. The Company can provide no assurance as
to the timing and the outcome of any of these proceedings. A decision by a
court in the United States or in any other jurisdiction in a manner adverse to
the Company could have a material adverse effect on the Companys business,
financial condition and results of operations. The Company has not
established any reserves or provisions for these legal proceedings. Replagal Patent Litigation In July 2000, Genzyme and Mount Sinai filed a patent infringement action
against the Company in the United States District Court of Delaware. The
complaint alleges that the Companys activities relating to Replagal infringe a
patent licensed by Genzyme from Mount Sinai. In January 2002, the United States
District Court of Delaware dismissed this patent litigation granting the
Companys motion for summary judgment of non-infringement and denying Genzyme
and Mount Sinais motion for summary judgment of infringement. Genzyme and
Mount Sinai sought monetary damages and injunctive relief. In March 2002, Genzyme and Mount Sinai appealed the United States District
Court of Delawares ruling to the United States Court of Appeals for the
Federal Circuit, and in January 2003 the United States Court of Appeals for the
Federal Circuit heard oral arguments on the appeal. In October 2003, pursuant
to a global legal settlement, Genzyme agreed to withdraw from this suit and
paid the Company $1,555,000. Mount Sinai is not a party to the settlement. In
October 2003, the United States Court of Appeals for the Federal Circuit
affirmed a finding of non-infringement by the Company. In January 2004, the
Federal Circuit denied Mount Sinais petition for a rehearing en banc. The
deadlines associated with further appeal have expired. 8




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Dynepo Patent Litigation In July 1999, the Company commenced legal proceedings with Aventis in the
United Kingdom against Kirin-Amgen, Inc. (Kirin-Amgen), which sought a
declaration that a U.K. patent held by Kirin-Amgen will not be infringed by the
Companys activities relating to Dynepo and that certain claims of
Kirin-Amgens U.K. patent are invalid. In April 2001, the High Court of Justice
in the United Kingdom ruled that Dynepo infringed one of four claims of the
patent asserted by Kirin-Amgen. In July 2002, the Court of Appeals in the
United Kingdom reversed the High Court of Justice and ruled that Dynepo did not
infringe Kirin-Amgens patent. Kirin-Amgen petitioned the House of Lords to
hear an appeal from the decision of the Court of Appeals. The House of Lords
agreed to hear this appeal during the summer of 2004. Although Kirin-Amgens
U.K. patent expires in December 2004, if Kirin-Amgens appeal to the House of
Lords is successful, Kirin-Amgen will have the right to seek a post-expiry
injunction against Aventis and the Company to preclude Aventis and the Company
from manufacturing or selling Dynepo in the United Kingdom for a period of time
after the U.K. patent expires equal to the period during which Kirin-Amgen
alleges that the Company and Aventis infringed the U.K. patent. In addition, in April 1997, Amgen Inc. (Amgen) commenced a patent
infringement action against the Company and Aventis in the United States
District Court of Massachusetts. In January 2001, the United States District
Court of Massachusetts concluded that Dynepo infringed eight of the 18 claims
of five patents that Amgen had asserted. Amgen did not seek and was not awarded
monetary damages. In January 2003, the United States Court of Appeals for the Federal Circuit
issued a decision affirming in part and reversing in part the decision of the
United States District Court of Massachusetts and remanded the action to the
United States District Court of Massachusetts for further proceedings. In
particular, the United States Court of Appeals for the Federal Circuit:  upheld the United States District Court of Massachusetts determination
of invalidity of one of Amgens patents;  upheld the United States District Court of Massachusetts determination
that some claims of two other Amgen patents were infringed, but vacated
the United States District Court of Massachusetts determination that
those patents were not invalid; and  vacated the United States District Court of Massachusetts determination
that Dynepo infringed some claims of the two remaining Amgen patents, and
vacated the United States District Court of Massachusetts determination
that one of these patents was not invalid. As part of the United States Court of Appeals for the Federal Circuits ruling,
it remanded the case to the United States District Court of Massachusetts and
instructed it to reconsider the validity of Amgens patents in light of
potentially invalidating prior art. The United States District Court of
Massachusetts has concluded the remand proceedings and heard oral argument on
some of these issues in July 2003. The Company expects that the United States
District Court of Massachusetts will enter a decision on the remanded issues at
some point during the first half of 2004. The United States District Court of
Massachusetts also recently issued a decision upholding its earlier findings
that Amgen successfully rebutted the presumption of prosecution history
estoppel with respect to certain of its patents, and therefore, that the
Company and Aventis infringe such patents in light of recent Supreme Court
precedents. On remand, the Company and Aventis presented affirmative defenses
with respect to such patents. The Company, Amgen and Aventis all have the right
to appeal the decision of the United States District Court of Massachusetts to
the United States Court of Appeals for the Federal Circuit. In March 2004, the Company amended its license agreement with Aventis relating
to Dynepo. Under the amended license agreement Aventis retained the right to
control the Amgen litigation in the United States and agreed to assume
responsibility for 100% of the litigation costs incurred with respect to both
the United States litigation and the Kirin-Amgen litigation in the United
Kingdom prior to March 26, 2004. Aventis will pay all U.S. litigation expenses
incurred from and after March 26, 2004, but the Company is required to
reimburse Aventis for 50% of these litigation costs. Aventis is entitled to
deduct up to 50% of any royalties that Aventis may otherwise owe the Company
with respect to the sale of Dynepo until Aventis has recouped the full amount
of the Companys share of the U.S. litigation costs. The Company has the right
to control the U.K. litigation and is responsible for all litigation costs
incurred with respect to such litigation and any other litigation
that might arise outside of the United States from and after March 26, 2004. Purported Class Action Shareholder Suit 9




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In January and February 2003, various parties filed purported class action
lawsuits against the Company and Richard Selden, the Companys former Chief
Executive Officer, in the United States District Court for the District of
Massachusetts. The complaints generally allege securities fraud during the
period from January 2001 through January 2003. Each of the complaints asserts
claims under Section 10(b) of the Securities Exchange Act of 1934, Rule 10b-5
promulgated thereunder, and Section 20(a) of the Exchange Act, and alleges that
the Company and its officers made false and misleading statements and failed to
disclose material information concerning the status and progress for obtaining
United States marketing approval of the Companys Replagal product to treat
Fabry disease during that period. In March 2003, various plaintiffs filed motions to consolidate, to appoint lead
plaintiff, and to approve plaintiffs selections of lead plaintiffs counsel.
In April 2003, various plaintiffs filed a Joint Stipulation and Proposed Order
of Lead Plaintiff Applicants to Consolidate Actions, To Appoint Lead Plaintiffs
and to Approve Lead Plaintiffs Selection of Lead Counsel, Executive Committee
and Liaison Counsel. In April 2003, the Court endorsed the Proposed Order,
thereby consolidating the various matters under one matter: In re Transkaryotic
Therapies, Inc., Securities Litigation, C.A. No. 03-10165-RWZ. In July 2003, the plaintiffs filed a Consolidated and Amended Class Action
Complaint, which the Company refers to as the Amended Complaint, against the
Company; Dr. Selden; Daniel Geffken, the Companys former Chief Financial
Officer; Walter Gilbert, Jonathan S. Leff, Rodman W. Moorhead, III, and Wayne
P. Yetter, members of the Companys board of directors; William R. Miller and
James E. Thomas, former members of the Companys board of directors; and SG
Cowen Securities Corporation, Deutsche Bank Securities Inc., Pacific Growth
Equities, Inc. and Leerink Swann & Company, underwriters of the Companys
common stock in prior public offerings. The Amended Complaint alleges securities fraud during the period from January
4, 2001 through January 10, 2003. The Amended Complaint alleges that the
defendants made false and misleading statements and failed to disclose material
information concerning the status and progress for obtaining United States
marketing approval of Replagal during that period. The Amended Complaint
asserts claims against each of the defendants under Section 11 of the
Securities Act of 1933 and against Dr. Selden under Section 15 of the
Securities Act; against SG Cowen Securities Corporation, Deutsche Bank
Securities, Pacific Growth Equities, Inc., and Leerink Swann & Company under
Section 12(a)(2) of the Securities Act; against Dr. Selden and us under Section
10(b) of the Exchange Act and Rule 10b-5 promulgated thereunder; and against
Dr. Selden under Section 20(a) of the Exchange Act. The plaintiffs seek
equitable and monetary relief, an unspecified amount of damages, with interest,
and attorneys fees and costs. In September 2003, the Company filed a motion to dismiss the Amended Complaint.
A hearing of the motion occurred in December 2003. A class has not been
certified, and the court has not made any decision on the motion. As of March 31, 2004,
the Company had spent approximately $1,100,000 related to
this lawsuit and shareholder derivative suit described below. The Company
expects that future costs related to these suits will be significant. Shareholder Derivative Suit In April 2003, South Shore Gastrointerology UA 6/6/1980 FBO Harold Jacob, and
Nancy R. Jacob Ttee filed a Shareholder Derivative Complaint against Dr.
Selden; against the following members of the Companys board of directors:
Jonathan S. Leff, Walter Gilbert, Wayne P. Yetter, Rodman W. Moorhead III;
against the following former members of the Companys board of directors: James
E. Thomas, and William Miller; and against the Company as nominal defendant, in
Middlesex Superior Court in the Commonwealth of Massachusetts, Civil Action No.
03-1669. On May 29, 2003, the parties moved to transfer venue to the Business
Litigation Session in Suffolk Superior Court in the Commonwealth of
Massachusetts. The parties motion was allowed, and in June 2003 the matter was
accepted into the Business Litigation Session as Civil Action No. 03-02630-BLS. The complaint alleges that the individual defendants breached fiduciary duties
owed to the Company and its shareholders by disseminating materially false and
misleading statements to the market and causing or allowing the Company to
conduct its business in an unsafe, imprudent and unlawful manner. The complaint
purports to assert derivative claims against the individual defendants for
breach of fiduciary duty, and to assert a claim for contribution and
indemnification on behalf of the Company for any liability the Company incur as
a result of the individual defendants alleged misconduct. The complaint seeks
declaratory, equitable and monetary relief, an unspecified amount of damages,
with interest, and attorneys fees and costs. In August 2003, the plaintiff filed its Verified Amended Derivative Complaint,
which the Company refers to as the Amended Derivative Complaint. The Amended
Derivative Complaint alleges that the individual defendants breached fiduciary
duties owed to the Company and its stockholders by causing the Company to issue
materially false and misleading statements to the public, by signing the
Companys Form 10-Ks for the years 2000 and 2001 and by signing a registration
statement. The Amended Derivative Complaint also alleges that defendant Dr.
Selden sold the Companys stock while in possession of material non-public
information. The plaintiffs seek declaratory, equitable and monetary relief, an
unspecified amount of damages, with interest, and attorneys fees and costs. 10




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In September 2003, the Company served a motion to dismiss the Amended
Derivative Complaint. A hearing of the motion was held in
January 2004. In May 2004, the Court granted the Companys
motion to dismiss. The plaintiffs may appeal the ruling. As of March 31, 2004,
the Company had spent approximately $1,100,000 related to
this lawsuit and the purported class action shareholder suit described above.
The Company expects that future costs related to these suits will be
significant. SEC Investigation In May 2003, the Company received a copy of a formal order of investigation by
the Securities and Exchange Commission. The order of investigation relates to
the Companys disclosures and public filings with regard to Replagal and the
status of the FDAs approval process for Replagal, as well as transactions in
the Companys securities. The Company is cooperating fully and will continue to
cooperate fully with the SEC in the investigation. As of March 31, 2004, the
Company had spent approximately $1,400,000 related to this matter. 9. SUBSEQUENT EVENT On May 4, 2004, the Company sold $90,000,000 principal amount of 1.25% senior
convertible notes due 2011 (the Notes). The Company granted to the
underwriters of the offering of the Notes an overallotment option to purchase
an additional $10,000,000 principal amount of the Notes within 30 days of the
offering. The Company received net proceeds amounting to approximately
$87,300,000. Holders of the Notes may convert the Notes at any time into
shares of the Companys common stock at an initial conversion rate of 54.0972
shares of common stock per $1,000 principal amount of notes, which is
equivalent to a conversion price of approximately $18.49 per share of common
stock, prior to the close of business on May 14, 2011. The Company may redeem
the Notes, in whole or in part, at any time on or after May 20, 2007 and before
May 20, 2009 at redemption price equal to 100% of the principal amount of the
notes, plus accrued and unpaid interest, and other adjustments. On or after
May 20, 2009, the Company may redeem for cash all or part of the Notes. Unless
the Notes are redeemed, repaid or converted, the Notes will mature on May 15,
2011 at their principal amount. The Company intends to use the net proceeds
from the sale of the Notes for general corporate purposes, including the
expected purchase of the holdings of the minority interest in TKT
Europe-SS AB, the Companys 80%-owned European subsidiary
(TKT Europe). 11




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ITEM 2. MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
RESULTS OF OPERATIONS Overview Transkaryotic Therapies, Inc. (the Company or TKT) is a biopharmaceutical
company researching, developing and commercializing therapeutics, primarily for
the treatment of rare genetic diseases caused by protein deficiencies. TKT has
approval to market and sell Replagal (agalsidase alfa), an enzyme replacement
therapy for the long-term treatment of patients with Fabry disease, in 28
countries outside of the United States. The Company recorded $17,372,000 of
product sales of Replagal in the three months ended March 31, 2004. The
Companys two most advanced active clinical programs include
iduronate-2-sulfatase (I2S), an enzyme replacement therapy for the treatment
of Hunter syndrome, and Gene Activated glucocerebrosidase (GA-GCB), an enzyme
replacement therapy for the treatment of Gaucher disease. The Company is
currently conducting a pivotal clinical trial of I2S and initiated a Phase I/II
clinical trial of GA-GCB in April 2004. TKT is currently evaluating
out-licensing opportunities for GA-GCB as well as a number of other
gene-activated and gene therapy products. Outside its focus on rare diseases,
TKT intends to commercialize Dynepo, its Gene-Activated erythropoietin product
for anemia related to kidney disease, in the European Union. With the exception of 1995, the Company has incurred substantial annual
operating losses since inception. The Company expects to incur significant
operating losses until substantial product sales are generated. Until such
time, the Company is dependent upon product sales, collections of accounts
receivable, existing cash resources, interest income, external financing from
equity offerings, debt financings, and collaborative research and development
alliances to finance its operations. At March 31, 2004, the Companys
accumulated deficit was $454,819,000. The Company expects that its existing
capital resources, together with the net proceeds from the sale of of the 1.25%
Senior Convertible Notes due 2011 (the Notes), as discussed in Liquidity and
Sources of Capital, and anticipated proceeds from collections on existing
accounts receivable, anticipated cash payments under collaborative agreements,
and interest income, will be sufficient to fund its operations into 2006. The Companys results of operations may vary significantly from period to
period depending on, among other factors:  the timing and amount of Replagal product sales, as well as the cash
collections on receivables;  continued progress in TKTs research and development programs,
particularly with respect to I2S and GA-GCB;  the Companys ability to commence the manufacturing of Dynepo on a
timely and cost-effective basis and the timing and commercial success of
the launch of Dynepo in the European Union;  the scope and results of the Companys clinical trials;  the timing of, and the costs involved in, obtaining regulatory
approvals;  the cost of expansion of the Companys internal manufacturing
facilities;  the inherent variability of product yields in biological manufacturing
activities;  fluctuations in foreign exchange rates for sales denominated in
currencies other than the United States dollar;  the quality and timeliness of the performance of third party suppliers;  the cost of commercialization activities, including product marketing,
sales and distribution;  the costs involved in preparing, filing, prosecuting, maintaining, and
enforcing patent claims and other patent-related costs, including
litigation costs and the results of such litigation;  the outcome of pending purported class action and other related, or
potentially related, actions and the litigation costs with respect to such
actions;  the timing and cost of TKTs purchase of the minority interest in the
Companys 80%-owned European subsidiary, TKT Europe  5S AB (TKT
Europe);  the outcome of the Securities and Exchange Commission (the SEC)
investigation referred to in the notes to the condensed, consolidated
financial statements; and  the Companys ability to establish and maintain collaborative
arrangements.   12




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Recent Product Development and Business Activities In March 2004, the Company amended its license agreement with Aventis relating
to Dynepo. Under the amended agreement, TKT regained exclusive rights to make,
use and sell Dynepo outside the United States and licensed from Aventis the
Dynepo trademark. Under the amended agreement, TKT agreed to pay Aventis a
single-digit royalty on the Companys net sales of Dynepo outside of the United
States. TKTs royalty obligation expires, on a country-by-country basis, on
the later of 10 years after the first commercial sale of Dynepo in such country
and the date of expiration of the last to expire of the patents covering Dynepo
in such country. Under the amended agreement, Aventis retained its exclusive right to make, use
and sell Dynepo in the United States and is obligated to pay the Company a low
double-digit royalty on its net sales of Dynepo in the United States. Aventis
has also agreed to pay the Company $8,000,000 upon the achievement of a
specified U.S. commercial milestone. The Company has granted to Aventis a
one-year right of first refusal to purchase or license any of the Companys
gene therapy programs that the Company determines to sell or license. Before the Company can market and sell Dynepo in the European Union, the
Company will need to establish manufacturing capabilities for Dynepo outside of
the United States and sales and marketing capabilities for Dynepo in the
European Union. Specifically, the Company will need to enter into arrangements
with contract manufacturers, work with contract manufacturers to set up and
validate manufacturing processes and obtain the approval of the European
Commission of an amendment to the approved marketing authorization applications
(MAA) for Dynepo reflecting the new manufacturing sites. The Company intends
to commercialize Dynepo by either expanding its existing sales and marketing
infrastructure in Europe or entering into arrangements with third parties for
the sales and marketing of Dynepo. The Company and Aventis have been involved in patent infringement actions with
Kirin-Amgen, Inc. (Kirin-Amgen) and Amgen Inc. (Amgen) involving Dynepo
which is described under Note 8 to the condensed, consolidated financial
statements. Under the amended agreement, Aventis retained the right to control
the litigation in the United States and agreed to assume responsibility for
100% of the litigation costs incurred with respect to both the United States
litigation and the litigation in the United Kingdom prior to March 26, 2004.
Aventis will pay all U.S. litigation expenses incurred from and after March 26,
2004, but TKT is required to reimburse Aventis for 50% of these litigation
costs. Aventis is entitled to deduct up to 50% of any royalties that Aventis
may otherwise owe the Company with respect to the sale of Dynepo until Aventis
has recouped the full amount of TKTs share of the U.S. litigation costs. The
Company has the right to control the U.K. litigation and is responsible for all
litigation costs incurred with respect to such litigation and any other
litigation that may arise outside of the United States from and after March 26,
2004. The Company currently estimates that its share of the expenses
associated with this litigation will be significant. Application of Critical Accounting Policies and Estimates The discussion and analysis of TKTs financial condition and results of
operations is based on the Companys consolidated financial statements, which
have been prepared in accordance with accounting principles generally accepted
in the United States. The preparation of these financial statements requires
TKT to make estimates and judgments that affect its reported assets and
liabilities, revenues and expenses, and other financial information. Actual
results may differ significantly from these estimates under different
assumptions and conditions. In addition, TKTs reported financial condition and
results of operations could vary due to a change in the application of a
particular accounting standard. The Company regards an accounting estimate underlying its financial statements
as a critical accounting estimate if the accounting estimate requires the
Company to make assumptions about matters that are highly uncertain at the time
of estimation and if different estimates that reasonably could have been used
in the current period, or changes in the estimate that are reasonably likely to
occur from period to period, would have had a material effect on the
presentation of financial condition, changes in financial condition, or results
of operations. Revenue Recognition The Company recognizes revenue from product sales in accordance with Staff
Accounting Bulletin 104 (SAB 104), Revenue Recognition, when there is
persuasive evidence that an arrangement exists, delivery has occurred, the
price is fixed or determinable, and collection is reasonably assured. The
Company determines that collection is reasonably assured in Europe and in some
other countries outside of the United States, once reimbursement agreements and
pricing arrangements are established and formalized, as these agreements
establish the relevant governmental agencys intent to pay, or once there are
legally binding purchase agreements between a hospital and the Company, or once
approval has been granted for the reimbursement of cost for individual
patients. The Company only records revenues in those countries for which one of
the conditions set forth in the previous sentence has been met. If any of the
above circumstances were to change, it could affect the Companys revenue
recognition in future periods. During the first quarter of 2004, the Company recorded a $481,000 reversal of
2003 price discount accrual to product sales, as the 13




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Company determined it was no longer probable that this amount would be paid to
customers. The Companys significant accounting policies are described in the Notes to the
Consolidated Financial Statements in the Companys Annual Report on Form 10-K
for the year ended December 31, 2003, which is on file with the SEC. The
Company regards its policies with respect to revenue recognition, accounts
receivable, inventories, asset impairment and restructuring charges as
critical accounting estimates. There have been no changes to such policies or
significant changes in assumptions or estimates that would affect such policies
in the first quarter of 2004. These policies are described under the caption
Item 7 Managements Discussion and Analysis of Financial Condition and Results
of Operations in the Companys Annual Report on Form 10-K for the year ended
December 31, 2003. Results of Operations The following discussion of the financial condition and results of operations
of the Company should be read in conjunction with the accompanying condensed,
consolidated financial statements and the related notes thereto. Revenues Revenues for the quarters ended March 31, 2004 and 2003 were: Three months ended March 31,
    
    2004 vs. 2003(in thousands, except percentages)
    
    2004
    
    2003
    
    $ Change
    
    % ChangeProduct sales
    
    $
    17,372
    
    
    $
    12,169
    
    
    $
    5,203
    
    
    
    43
    %License and research revenues
    
    
    62
    
    
    
    14
    
    
    
    48
    
    
    
    343
    %$
    17,434
    
    
    $
    12,183
    
    
    $
    5,251
    
    
    
    43
    %
 Product Sales Substantially all Replagal product sales were in Europe. The increase in sales
in the first quarter of 2004 over the comparative periods in 2003 reflects an
overall increase in unit sales and the impact of foreign currency fluctuations
as described below. A reversal of a 2003 price discount accrual during the
first quarter of 2004 contributed approximately $481,000 to first quarter 2004
product sales as the Company determined it was no longer probable that this
amount would be paid to customers. The Company prices Replagal in the functional currency of the country into
which it is sold. While overall price levels in local currencies are generally
consistent period over period, foreign exchange fluctuations caused
an increase in the United States dollar denominated average selling prices. In
the first quarter of 2004, foreign currency fluctuations increased sales and
gross margins by approximately $2,400,000, or 20%, as compared to the first
quarter of 2003. Substantially all of the Companys manufacturing costs are
in United States dollars. Therefore, any fluctuation in the value of the
payment currencies relative to the United States dollar is likely to impact
gross margins since the Companys manufacturing costs would remain
approximately the same while its revenue in terms of United States dollars
would change. The Companys gross margin will continue to be affected by
currency fluctuations in the future. Product sales and gross margins will be negatively affected if the U.S. dollar
strengthens against currencies in which the Company sells Replagal. The Company
currently does not engage in foreign currency hedging activities. License and Research Revenues The increase in license and research revenues in the first quarter 2004 from
the corresponding period in 2003 was due to the global legal settlement and
distribution agreements that the Company executed with Genzyme Corporation
(Genzyme) in the fourth quarter of 2003. During the fourth quarter of 2003,
the Company received $3,055,000 from the agreements with Genzyme which was
recorded as deferred revenue. The Company records this deferred revenue as
license and research revenue ratably over a thirteen year period, representing
the term of the agreement over which the Company will supply bulk drug
substance. Cost of Goods Sold Components of cost of goods sold are as follows: 14




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Three months ended March 31,
    
    2004 vs. 2003(in thousands, except percentages)
    
    2004
    
    2003
    
    $ Change
    
    % ChangeCost of product sales
    
    $
    2,236
    
    
    $
    2,669
    
    
    $
    (433
    )
    
    
    -16
    %Termination of contract
manufacturing agreement and
related charges
    
    
    
    
    
    
    832
    
    
    
    (832
    )
    
    
    -100
    %Cost of goods sold
    
    $
    2,236
    
    
    $
    3,501
    
    
    $
    (1,265
    )
    
    
    -36
    %Cost of goods sold as a percentage
of product sales
    
    
    13
    %
    
    
    29
    %
 For the three months ended March 31, 2004, cost of goods sold totaled
$2,236,000, or 13% of product sales, a decrease of $1,265,000 from $3,501,000,
or 29% of product sales, in the corresponding period in 2003. Cost of goods
sold consists of expenses incurred in connection with the manufacture of
Replagal. The decrease in cost of goods sold as a percentage of sales for the
quarter ended March 31, 2004 reflected continuing improvements in manufacturing
and production efficiencies as well as the contribution of foreign
currency fluctuations to product sales. This decrease also reflects the fact that the Company
incurred charges amounting to $832,000, or 7% of product sales, in the first
quarter of 2003 related to excess capacity at the terminated contract
manufacturer of bulk drug substance of Replagal. The Company has historically relied on contract manufacturing arrangements with
third parties for the production of Replagal bulk drug substance for commercial
sale, as well as contract packaging and labeling services. In January 2003, the
Company terminated its agreement with a third party manufacturer of the bulk
drug substance of Replagal, effective in July 2003. In July 2003, the European
Commission approved the Companys manufacturing facility at Cambridge,
Massachusetts (the Alewife Facility) for the
commercial manufacture of bulk drug substance for Replagal. In October 2003,
the Company began significant renovations to its manufacturing facility in the
Alewife Facility in order to expand its capacity and configure the facility for
the production on a commercial scale of products other than Replagal. In
anticipation of these renovations, in the third quarter of 2003, the Company
ceased all manufacturing operations at the Alewife Facility. Production at the
Alewife Facility is scheduled to recommence in the second half of 2004. At the
present time, the Company anticipates that existing inventory will be
sufficient to fill customer orders for Replagal into 2005. The Company will
continue to rely on third party manufacturers for preparation and packaging
services. The Company expects that Replagal inventory produced both at the contract
manufacturer and at the Companys Alewife Facility will be sold in 2004. Cost
of goods sold will reflect a mix of full production costs with respect to
inventory produced at the contract manufacturer, and partial production costs
with respect to inventory manufactured at the Alewife Facility as the majority
of such costs were previously expensed. The Company expects the cost of goods
sold percentage for 2004 will be approximately 20% of product sales. Research and Development Expenses Research and development expenses decreased by $1,145,000, or 5%, to
$19,837,000 in the first quarter of 2004, as compared to $20,982,000 during the
same period in 2003. The decrease primarily reflects the decreases in research
and development staffing and in outside testing and supplies costs in
connection with the Companys restructuring plan. The decrease also reflects
the fact that during the first quarter of 2003, the Company incurred
approximately $1,700,000 in contract manufacturing costs related to the
termination of a contract manufacturing agreement. The decrease in research
and development costs was partially offset by increases in clinical trial
expenses primarily related to the Companys I2S pivotal trial which was
initiated during the third quarter of 2003, and the start-up costs for the
GA-GCB phase I/II trial which the Company initiated in April 2004. The Company
expects its research and development costs will continue to increase relative
to the first quarter of 2004, primarily as expenditures are expected to
increase for the I2S and GA-GCB clinical trials, and for the manufacture of I2S and
GA-GCB for use in these
studies upon the completion of renovations to the Alewife Facility. The Company is currently seeking to enter into a contract manufacturing agreement
in Europe to produce its Dynepo product outside the United States. This will
result in increases in future research and development expenses. Research and
development costs for Dynepo are not reasonably certain because such costs are
dependent on a number of variables, including costs related to technology
transfers, costs associated with the startup of Dynepo manufacturing, and
uncertainties in the timing and approval of the manufacturing facility and
processes. The Companys two largest research and development programs, Replagal and I2S,
represent the majority of the Companys research and development spending. The
expenses associated with these programs totaled approximately 63% of total
research and development expenses for the three months ended March 31, 2004, as
compared to 70% of total research and development expenses for the
corresponding period in 2003. Expenses associated with the Companys
preclinical and clinical programs related to the Companys products for the
treatment of other rare genetic diseases, and Gene-Activated protein products,
accounted for the balance of the Companys research and development expenses
for the three months ended March 31, 2004. For the three months ended March 31, 2004, research and development expenses
for the Replagal program totaled $5,502,000, a decrease of $1,221,000, or 18%,
from $6,723,000 in the corresponding period of 2003. The decrease in the 2004
period is primarily due to the Companys decision to cease efforts to seek the
approval of Replagal in the United States from the United States Food and Drug
Administration (the FDA). The Company expects the amount of future
Replagal-related research and development expenses 15




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will decrease significantly. The Company will continue to incur expenses
related to the conditions associated with the Companys European and Canadian
approvals of Replagal, including European obligations to conduct additional
clinical trials and to submit an annual assessment of Replagal for review by
regulatory authorities. Future Replagal-related expenditures are principally
dependent upon those regulatory requirements. For the three months ended March 31, 2004, research and development expenses
for the I2S program totaled $6,920,000, a decrease of $959,000 or 12% from
$7,879,000 in the corresponding period of 2003. The decrease in the first
quarter of 2004 was primarily due to the renovation of the Alewife Facility,
which resulted in no production of materials for the I2S clinical trials. This
decrease was partially offset by increases in expenses related to the Companys
I2S pivotal clinical trial for which enrollment was completed in the first
quarter of 2004. Future research and development costs for the I2S program are not reasonably
certain because such costs are dependent on a number of variables, including
the cost and design of any additional clinical trials, uncertainties in the
timing of the regulatory process, and the costs associated with large-scale
manufacture of I2S. The Company estimates that the cost of its pivotal
clinical trial of I2S may aggregate approximately $10,000,000 to $15,000,000 in
2004. The Company expects that expenses related to I2S will be significant in
2004 as the Company intends to prepare applications for marketing approval of
I2S. Intellectual Property License Fee Expense In June 2002, the Company obtained an exclusive license to certain patents and
patent applications from Cell Genesys, Inc. (Cell Genesys) related to Cell
Genesys approach to gene activation. In consideration for the license, the
Company initially paid Cell Genesys $11,000,000 in cash and issued to Cell
Genesys shares of the Companys common stock worth $15,000,000 as of the date
of the agreement. Under the license agreement, the Company agreed that the number of shares of
common stock initially issued to Cell Genesys would be adjusted at the time the
Company registered such shares for resale under the Securities Act of 1933, as
amended, if the market value of such shares at that time was greater or less
than $15,000,000. Pursuant to the agreed upon formula, at December 31, 2002,
with the closing price of the Companys common stock at $9.90 per share, the
Company would have been required to issue to Cell Genesys an additional
1,148,000 shares of common stock. As a result, the Company recorded an
additional non-cash license fee expense of $8,660,000 in the fourth quarter of
2002. On January 15, 2003, the Company and Cell Genesys renegotiated the
consideration paid for the license, and the Company repurchased the shares of
stock issued to Cell Genesys for $15,000,000 in cash. The Company incurred an
additional license expense in the first quarter of 2003 of $1,350,000, which
represents the further decline in the market value of the Companys common
stock from December 31, 2002 to January 15, 2003. The repurchased shares have
been recorded as treasury stock. Under the license agreement, Cell Genesys also has the potential to receive
certain milestone payments from the Company contingent upon the outcome of
related patent matters under the license agreement. If all of the milestones
are achieved, the Company will be obligated to pay Cell Genesys an aggregate of
$17,000,000 payable in part in cash and in part in stock. The Company cannot
predict when those milestones will become due, if ever. The Company is not
required to make royalty payments to Cell Genesys. Selling, General and Administrative Expenses The Companys selling, general and administrative expenses were as follows: Three months ended March 31,
    
    2004 vs. 2003(in thousands, except percentages)
    
    2004
    
    2003
    
    $ Change
    
    % ChangeGeneral and administrative
    
    $
    4,133
    
    
    $
    5,160
    
    
    $
    (1,027
    )
    
    
    -20
    %Selling and marketing
    
    
    4,825
    
    
    
    4,006
    
    
    
    819
    
    
    
    20
    %Selling, general and administrative expenses
    
    $
    8,958
    
    
    $
    9,166
    
    
    $
    (208
    )
    
    
    -2
    %
 For the three months ended March 31, 2004, selling, general and administrative
expenses were $8,958,000, a decrease of $208,000, from $9,166,000 for the
corresponding period in 2003. This decrease reflects executive severance
charges incurred in the first quarter of 2003, and legal costs in connection
with the Companys shareholder lawsuits and SEC investigation incurred during
the first quarter of 2003 which were incurred at a higher level than in the
first quarter of 2004. The overall decrease was partially offset by increases 16




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in selling and marketing expenses related to ongoing Replagal sales and
marketing efforts by TKT Europe as well as approximately $600,000 in foreign
currency fluctuations, due to strengthening United States dollar relative to
the Swedish Krona. The Company expects selling, general and administrative expenses related to
selling and marketing expenses to continue to increase in 2004 as the Company
establishes infrastructure and distribution capabilities to support
commencement of Replagal product sales in additional countries outside of the
European Union. In addition, the Company expects to incur transition costs
related to the buyout of the minority interest in TKT Europe. The Company is currently evaluating potential commercialization strategies for
Dynepo in Europe, which could contribute to increases in future selling,
general and administrative expenses. The Company expects this evaluation will
take 18 to 24 months to complete. Future selling, general and administrative
costs for Dynepo are not reasonably certain because such costs are dependent on
a number of variables, including the costs to build commercial and distribution
infrastructure, and costs related to enter into and support potential sales and
marketing licensing agreements with third parties. Restructuring Charges In February 2003, the Company announced a major reorganization in an effort to
reduce costs and narrow the scope of the Companys research initiatives. As
part of this restructuring, during the first quarter of 2003, the Company
reduced its United States headcount by approximately 100 positions and
consolidated four of its facilities throughout 2003. The Companys
restructuring actions were substantially complete as of December 31, 2003. Restructuring charges amounted to $861,000 and $3,602,000 for the three months
ended March 31, 2004 and 2003, respectively. In the first quarter of 2004,
the Company recorded $861,000 of restructuring charges related to ongoing
facility and lease expenses related to the four vacated facilities. Included
in the first quarter 2003 charge is $1,332,000 of employee severance and
outplacement services costs for 74 employees, primarily in research and
development, and $2,270,000, representing the remaining lease obligation for
one of the four facilities that the Company no longer occupies. The Company
will continue to record restructuring charges primarily related to vacated
facility expenses during the remainder of the lease terms until such facilities
are sublet. Interest Income Interest income was $308,000 and $776,000 for the three months ended March 31,
2004 and 2003, respectively. The decrease in interest income for the first
quarter of 2004 as compared to the same period in 2003 was primarily due to the
decrease in cash and marketable securities balances and lower rates of return.
During the first quarter of 2004, average cash, cash equivalents, and
marketable securities balances were $170,666,000 as compared to $231,400,000
for the same period of 2003. The Company expects incremental growth in
interest income due to an increase in cash and marketable securities reflecting
proceeds from the Notes offering. Minority Interest The Company recorded minority interest charges in the net loss of TKT Europe of
$1,000 during the three months ended March 31, 2004. To date, the Company has
recorded minority interest charges amounting to $415,000 related to the
Companys 80% interest in the cumulative net income of TKT Europe. Net Loss The Company had a net loss of $14,151,000 and $25,945,000 for the three months
ended March 31, 2004 and 2003, respectively. Basic and diluted net loss per
share was $0.41 and $0.75 for the three months ended March 31, 2004 and 2003,
respectively. Liquidity and Sources of Capital Since its inception, TKT has financed its operations through:  
    
    the sale of common and preferred stock;
    
    borrowings under debt agreements;
    
    revenues from collaborative agreements;
    
    interest income; and
    
    more recently, with collections from accounts receivable and the sales of the Notes. 17




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On May 4, 2004, the Company sold $90,000,000 principal amount of Notes. The
Company granted to the underwriters of the offering of the Notes an
overallotment option to purchase an additional $10,000,000 principal amount of
the Notes within 30 days of the offering. In the near term, TKT expects to finance its operations principally from
existing cash and cash equivalents, collections of accounts receivable related
to sales of Replagal and from the proceeds of the sale of the Notes in April
2004. The Company expects that its existing capital resources, together with
anticipated collections on existing and future accounts receivable on product
sales, anticipated cash payments under collaborative agreements, proceeds from
the sale of the Notes, and interest income, will be sufficient to fund its
operations into 2006. Cash Flows The Company had cash, cash equivalents and marketable securities totaling
$164,634,000 at March 31, 2004, including restricted marketable securities
collateralizing letters of credit totaling $7,991,000 and not including
$87,300,000 net proceeds received in May 2004 from the sale of the Notes.
Included in such amount was $74,273,000 held by TKT Europe, which was primarily
denominated in Swedish Krona, British Pound, and Euro. Cash equivalents and
marketable securities are invested in United States government and agency
obligations and money market funds. The Company used net cash of $9,273,000 for operating activities in the first
quarter of 2004. Major cash flow changes consisted of a net loss of
$14,151,000, and depreciation expense of $2,924,000. Working capital at March
31, 2004, was $184,539,000 compared to $204,190,000 at December 31, 2003.
Accounts receivable decreased by $226,000 in the first quarter of 2004 due to
collections on accounts receivable for Replagal sales. Inventory decreased by
$1,561,000 in the first quarter of 2004 primarily due to product sales and a cessation of manufacturing
activity at the Companys Alewife Facility. In certain European countries, such as Italy and Belgium, customary payment
terms on accounts receivable are significantly longer than in the United
States, particularly for products treating orphan drug indications. In these
countries, the Company historically has received, and expects to continue to
receive, payments approximately one year from the invoice date. Accounts
receivable balances for Italy and Belgium were 56% and 49% of total accounts
receivable at March 31, 2004 and 2003, respectively. The Company monitors its
days sales outstanding and collections in these countries. To date, these
customers have been paying within the customary payment terms. If collections
and days sales outstanding in these countries deteriorate in the future, the
Companys liquidity will be adversely affected. Net cash used for investing activities was $5,710,000 for the quarter ended
March 31, 2004. The Company used $5,660,000 during the first quarter of 2004
for property and equipment purchases related to leasehold improvements and
equipment for the Companys manufacturing facility. The Company expects to
spend a total of approximately $14,000,000 for purchases of property and
equipment during the balance of 2004, principally for expanding its internal
manufacturing capabilities. The effect of exchange rate changes decreased cash and cash equivalents by $1,426,000 and is
primarily due to the strengthening United States dollar relative to the Swedish
Krona and the translation of our foreign subsidiaries cash and accounts
receivable balances, which are primarily denominated in the Euro currency. The Companys cash requirements for operating activities and investment
activities have significantly exceeded its internally generated funds. The
Company expects that its cash requirements for such activities will continue to
exceed its internally generated funds until it is able to generate
substantially greater product sales. The Company expects that it will require substantial additional funds to
support its research and development programs, obligations under license
agreements, acquisition of technologies, preclinical and clinical testing of
its products, pursuit of regulatory approvals, acquisition of capital
equipment, expansion of internal manufacturing capabilities, selling, general
and administrative expenses, and the buyout of the minority interests in TKT
Europe. On May 4, 2004, the Company sold $90,000,000 principal amount of 1.25% Senior
Convertible Notes with a scheduled maturity in 2011. The Company also granted
the underwriters an overallotment option to purchase up to an additional
$10,000,000 aggregate principal amount of the Notes. The Company received net
proceeds amounting to approximately $87,300,000, which will be used to fund
its operations and its expected purchase of the minority interest in
TKT Europe. The Company also plans to meet its long-term cash
requirements through anticipated proceeds from collections on existing accounts
receivable, anticipated cash payments under collaborative agreements, and
interest income. In December 2000 the Company filed a shelf registration statement on Form S-3
with the SEC, which became effective in December 2000. This shelf registration
statement permits the Company to offer, from time to time, any combination of
common stock, preferred stock, debt securities and warrants of up to an
aggregate of $500,000,000. Following the sale of the Notes, the Company had
approximately $132,000,000 worth of securities available for issuance under a
shelf registration statement. The Company may also pursue opportunities to
obtain additional external financing in the future through debt financing,
lease arrangements related to facilities and capital equipment, and
collaborative research and development agreements. 18




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If the Company is unable to obtain additional future financing, the Company may
be required to significantly curtail one or more of its research or development
programs or some of its commercial activities, which could harm the Companys
business, financial condition and operating results. The source, timing and
availability of any future financing will depend principally upon equity and
debt market conditions, interest rates and, more specifically, on the Companys
continued progress in its preclinical and clinical development programs, and
the extent of its commercial success. There can be no assurance that external
funds will be available on favorable terms, if at all. Contractual Obligations The Company has contractual obligations in the form of operating leases,
clinical trials contractual obligations, and equipment purchase commitments.
These contractual obligations at March 31, 2004 have not changed significantly
from December 31, 2003. In April 2000, the Company established TKT Europe for the purpose of marketing,
selling and distributing Replagal in Europe. Under the stockholders agreement
for TKT Europe, the Company is entitled to purchase the European stockholders
20% ownership interest in TKT Europe in September 2004, for a price determined
in accordance with a formula. Should the Company not exercise that right, the
European stockholders of TKT Europe can require the Company to purchase the
European stockholders ownership interest sixty days thereafter. The buyout
price is equal to (a) 20% of the operating profits, as defined in the
stockholders agreement, for the period from September 1, 2003 to August 31,
2004, multiplied by a buyout factor of four, subject to adjustment, plus (b)
20% of the accumulated positive earnings of TKT Europe. As a result, the amount
of the buyout price is dependent on the profits of TKT Europe and the
commercial success of Replagal in Europe. The Company estimates that the buyout
price could be between $55,000,000 and $65,000,000 based on the Companys
current estimates for sales and expenses. As of March 31, 2004, the Company had committed to pay approximately
$9,500,000 to various contract vendors for administering and executing
clinical trials. The timing of payments is not reasonably certain as payments
are dependent upon actual services performed by the organizations as determined
by patient enrollment levels and related activities. However, the Company does
expect to pay for these commitments throughout 2004 and into 2005 as ongoing
trials are completed. In June 2002, the Company obtained an exclusive license to certain patent and
patent applications from Cell Genesys related to Cell Genesys approach to gene
activation. In consideration for the license, the Company paid $11,000,000 cash
in June 2002 and an additional $15,000,000 in January 2003. If Cell Genesys
achieves all the milestones related to patent matters under the license
agreement, the Company will be obligated to pay Cell Genesys an aggregate of
$17,000,000 payable in part in cash and in part in stock. The Company cannot
predict when these milestones will become due, if ever. The Company is not
required to make royalty payments to Cell Genesys. Net Operating Loss Carryforwards At December 31, 2003, the Company had net operating loss carryforwards of
approximately $298,410,000, which expire at various times through 2023. Due to
the degree of uncertainty related to the ultimate use of loss carryforwards and
tax credits, the Company has fully reserved against any potential tax benefit.
The future utilization of net operating loss carryforwards and tax credits may
be subject to limitation under the changes in stock ownership rules of the
Internal Revenue Code. Because of this limitation, it is possible that taxable
income in future years, which would otherwise be offset by net operating
losses, will not be offset and, therefore, will be subject to tax. Litigation Expenses The Company is a party to the legal proceedings listed below which are
described in greater detail under Note 7 to the Condensed Consolidated
Financial Statements. The costs related to these proceedings have been
significant and the Company expects that these costs will continue to be
significant. The Company can provide no assurance as to the outcome of any of
these proceedings. A decision by a court in the United States or in any other
jurisdiction in a manner adverse to the Company could have a material adverse
effect on the Companys business, financial condition and results of
operations.  The Company has been engaged in patent litigation with Genzyme and
Mount Sinai with respect to Replagal. In October 2003, pursuant to a global
legal settlement, Genzyme agreed to withdraw from this patent litigation and
paid the Company $1,555,000. Mt. Sinai is not a party to the settlement. In
October 2003, the United States Court of Appeals for the Federal Circuit
affirmed a finding of non-infringement by the Company. In January 2004, the
Federal Circuit denied Mount Sinais petition for a rehearing en banc. The
deadlines associated with further appeal have expired. As of March 31,
2004, the Company had incurred approximately $4,687,000 in litigation expenses
associated with the Replagal litigation.  The Company and Aventis have been involved in patent infringement
actions with Kirin-Amgen and Amgen with respect to Dynepo. The litigation is
costly and the Company is required to reimburse Aventis, which is paying the
litigation expenses, for 50% of the 19




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expenses incurred in the
United States after March 26, 2004. Aventis is entitled to deduct up to 50% of any royalties due to the
Company from the sale of Dynepo until Aventis has recouped the full amount of
TKTs share of litigation expenses. The Company is responsible for all litigation expenses outside of the United
States incurred after March 26, 2004. The Company currently estimates that its
share of the expenses associated with the litigation will be significant.  In 2003 various parties filed purported class action lawsuits against
the Company, its former CEO, former CFO, the members of the Companys Board of
Directors and other parties. In April 2003 a derivative law suit was filed
against the Companys former CEO, the members of the Companys Board of
Directors and the Company as a nominal defendant, alleging that the individual
defendants breached fiduciary duties owed to the Company and its shareholders.
In May 2004, the Court granted the Company's motion to dismiss the derivative law
suit. The plaintiffs may appeal this ruling. As of March 31, 2004, the Company had incurred approximately $1,100,000
related to the shareholders law suit and derivative law suit.  In May 2003 the Company received a copy of a formal order of
investigation by the SEC. As of March 31, 2004, the Company had incurred
approximately $1,400,000 related to this matter. FORWARD-LOOKING STATEMENTS This quarterly report contains forward-looking statements within the meaning of
Section 27A of the Securities Act of 1933, as amended, and Section 21E of the
Exchange Act that involve risks and uncertainties. The Company may, in some
cases, use words such as project, believe, anticipate, plan, expect,
estimate, intend, should, would, could, will, or may, or other
words that convey uncertainty of future events or outcomes to identify these
forward-looking statements. There are a number of important factors that could
cause actual results to differ materially from the results anticipated by these
forward-looking statements. These important factors include those set forth
below under Certain Factors That May Affect Future Results. These factors
and the other cautionary statements made in this quarterly report should be
read as being applicable to all related forward-looking statements wherever
they appear in this quarterly report. If one or more of these factors
materialize, or if any underlying assumptions prove incorrect, the Companys
actual results, performance or achievements may vary materially from any future
results, performance or achievements expressed or implied by these
forward-looking statements. In addition, any forward-looking statements
represent the Companys estimates only as of the date this quarterly report was
filed with the Securities and Exchange Commission and should not be relied upon
as representing the Companys estimates as of any subsequent date. While the
Company may elect to update forward-looking statements at some point in the
future, the Company specifically disclaims any obligation to do so, even if its
estimates change. Certain Factors That May Affect Future Results The following important factors could cause actual results to differ from
those indicated by forward-looking statements made by the Company in this
quarterly report and elsewhere from time to time. Financing risks We have not been profitable and expect to continue to incur substantial losses. We have experienced significant operating losses since our inception in 1988.
As of March 31, 2004, our accumulated deficit was $454.8 million. We had net
losses of $14.2 million in the three months ended March 31, 2004, $75.2 million
in 2003, $129.8 million in 2002 and $70.2 million in 2001. We expect that we will continue to incur substantial losses and that, until we
have substantial product sales, our cumulative losses will continue to
increase. We recorded $17.4 million in product sales in the three months ended
March 31, 2004, $57.2 million in product sales in 2003 and $34.7 million in
product sales in 2002. We expect that the losses that we incur will fluctuate
from quarter to quarter and that these fluctuations may be substantial. We may need additional financing, which may be difficult to obtain. If we do
not obtain additional financing, our business, results of operations and
financial condition may be adversely affected. Our cash requirements for operating activities, financing activities and
investment activities have historically exceeded our internally generated
funds. We expect that our cash requirements for such activities will continue
to exceed our internally generated funds until we are able to generate
substantial product sales. We expect that our existing capital resources, together with the net proceeds
from the offering of the Notes, anticipated proceeds from collections on
existing accounts receivable, anticipated future product sales and margins on
such sales, anticipated cash payments under collaborative agreements, and
interest income, will be sufficient to fund our operations into 2006 and to
fund our expected purchase of the minority stockholders interest in our
majority-owned subsidiary in Europe, TKT Europe-5S AB, for between $55 million
and $65 million. However, our existing capital resources, the net proceeds from
the offering, and our other anticipated sources of capital may not provide
adequate funds to satisfy our capital requirements. Our future capital
requirements will depend on many 20




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factors, including the following:  the timing and amount of Replagal product sales, as well as the cash
collections on receivables;  continued progress in our research and development programs,
particularly with respect to iduronate-2-sulfate, or I2S, and
Gene-Activated glucocerebrosidase, or GA-GCB;  our ability to commence the manufacturing of Dynepo on a timely and
cost-effective basis and the timing and commercial success of the launch
of Dynepo in the European Union;  the scope and results of our clinical trials;  the timing of, and the costs involved in, obtaining regulatory
approvals;  the cost of expansion of our internal manufacturing facilities;  the inherent variability of product yields in biological manufacturing
activities;  fluctuations in foreign exchange rates for sales denominated in
currencies other than the United States dollar;  the quality and timeliness of the performance of third party suppliers;  the cost of commercialization activities, including product marketing,
sales and distribution;  the costs involved in preparing, filing, prosecuting, maintaining, and
enforcing patent claims and other patent-related costs, including
litigation costs and the results of such litigation;  the outcome of pending purported class action and other related, or
potentially related, actions and the litigation costs with respect to such
actions;  the timing and cost of our purchase of the minority interest in TKT
Europe;  the outcome of the SEC investigation referred to in the condensed,
consolidated financial statements; and  our ability to establish and maintain collaborative arrangements. Because we expect to incur substantial operating losses in the future, we may
need to seek additional funding for our operations. We may do so through
collaborative arrangements and public or private debt or equity financings.
Additional financing may not be available to us on acceptable terms, if at all.
If we do not obtain additional financing, our financial condition may be
adversely affected. If we raise additional funds by issuing equity securities, further dilution to
our then existing stockholders will result. If we raise additional funds by
issuing debt securities, our total indebtedness will increase and we may
subject ourselves to covenants that limit or restrict our ability to take
specified actions, such as incurring additional debt or making capital
expenditures. In addition, the terms of the financing may adversely affect the
holdings or the rights of our stockholders. If we are unable to obtain funding
on a timely basis, we may be required to significantly curtail one or more of
our research or development programs or some of our commercialization
activities. We also could be required to seek funds through arrangements with
collaborators or others that may require us to relinquish rights to certain of
our technologies, product candidates, or products which we would otherwise
pursue on our own. We have significant indebtedness and we may incur additional indebtedness in
the future. Our current indebtedness and any future indebtedness we incur
exposes us to risks that could adversely affect our business, operating results
and financial condition. We incurred $90 million of indebtedness when we sold the notes. We may also
incur additional long-term indebtedness or obtain working capital lines of
credit to meet future financing needs. This indebtedness could have significant
negative consequences for our business, operating results and financial
condition, including:  increasing our vulnerability to adverse economic and industry
conditions;  limiting our ability to obtain additional financing;  requiring the dedication of a substantial portion of our cash flow from
operations to service our indebtedness, thereby 21




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reducing the amount of our cash flow available for other purposes;  limiting our flexibility in planning for, or reacting to, changes in our
business; and  placing us at a possible competitive disadvantage with less leveraged
competitors and competitors that may have better access to capital
resources. If we experience a decline in revenues, we could have difficulty making
required payments on the notes and any indebtedness which we may incur in the
future. If we are unable to generate sufficient cash flow or otherwise obtain
funds necessary to make required payments, or if we fail to comply with the
various requirements of the notes or any indebtedness which we may incur in the
future, we would be in default, which would permit the holders of the notes and
any such indebtedness to accelerate the maturity of the notes and any such
indebtedness and could cause defaults under the notes or any such indebtedness
we may incur in the future. Any default under the notes or any indebtedness
which we may incur in the future could have a material adverse effect on our
business, operating results and financial condition. Our stock price has been and may in the future be volatile. This volatility may
make it difficult for you to sell common stock when you want or at attractive
prices. Our common stock has been and in the future may be subject to substantial price
volatility. The value of your investment could decline due to the effect of any
of the following factors upon the market price of our common stock:  announcements of technological innovations or new commercial products by
our competitors;  disclosure of results of clinical testing or regulatory proceedings by
us or our competitors;  results of litigation;  the timing, amount and receipt of revenue from sales of our products and
margins on sales of our products;  the timing of our expected purchase of, and the purchase price for, the
holdings of the minority stockholders in TKT Europe;  governmental regulation and approvals;  developments in patent or other proprietary rights;  public concerns as to the safety of products developed by us or the
fields of study in which we work; and  general market conditions. In addition, the stock market has experienced significant price and volume
fluctuations, and the market prices of biotechnology companies have been highly
volatile. Moreover, broad market and industry fluctuations that are not within
our control may adversely affect the trading price of our common stock. During
the period from January 1, 2002 to March 31, 2004, the closing sale price of
our common stock on the Nasdaq National Market ranged from a low of $3.74 per
share to a high of $46.50 per share. You must be willing to bear the risk of
fluctuations in the price of our common stock and the risk that the value of
your investment in our securities could decline. Our corporate governance structure, including provisions in our certificate of
incorporation and by-laws, our stockholder rights plan and Delaware law, may
prevent a change in control or management that securityholders may consider
desirable. Section 203 of the Delaware General Corporation Law and our certificate of
incorporation, by-laws and stockholder rights plan contain provisions that
might enable our management to resist a takeover of our company or discourage a
third party from attempting to take over our company. These provisions include
the inability of stockholders to act by written consent or to call special
meetings, and the ability of our board of directors to designate the terms of
and issue new series of preferred stock without stockholder approval. These provisions could have the effect of delaying, deferring, or preventing a
change in control of us or a change in our management that securityholders may
consider favorable or beneficial. These provisions could also discourage proxy
contests and make it more difficult for stockholders to elect directors and
take other corporate actions. These provisions could also limit the price that
investors might be willing to pay in the future for shares of our common stock
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If our clinical trials are not successful, we may not be able to develop and
commercialize our products, including I2S. In order to obtain regulatory approvals for the commercial sale of our
potential products, we and our collaborators will be required to complete
extensive clinical trials in humans to demonstrate the safety and efficacy of
our products. However, we may not be able to commence or complete these
clinical trials in any specified time period, or at all, either because the
U.S. Food and Drug Administration, or FDA, or other regulatory agencies object,
because we are unable to attract or retain clinical trial participants, or for
other reasons. Even if we complete a clinical trial of one of our potential
products, the data collected from the clinical trial may not indicate that our
product is safe or effective to the extent required by the FDA, the European
Commission, or other regulatory agencies to approve the potential product. For example, in November 2002, the FDA indicated to us that the data for
Replagal that we submitted in connection with our biologics license
application, or BLA, was not adequate for approval, and in January 2003, the
FDAs Endocrinologic & Metabolic Drugs Advisory Committee concluded that our
clinical data did not provide substantial evidence of efficacy. In January
2004, we withdrew our BLA for Replagal. The results from preclinical testing of a product that is under development may
not be predictive of results that will be obtained in human clinical trials. In
addition, the results of early human clinical trials may not be predictive of
results that will be obtained in larger scale, advanced-stage clinical trials.
Furthermore, we, one of our collaborators, or a regulatory agency with
jurisdiction over the trials may suspend clinical trials at any time if the
patients participating in such trials are being exposed to unacceptable health
risks, or for other reasons. The timing of completion of clinical trials is dependent in part upon the rate
of enrollment of patients. Patient accrual is a function of many factors,
including the size of the patient population, the proximity of patients to
clinical sites, the eligibility criteria for the study, the existence of
competitive clinical trials, and the availability of alternative treatments.
Delays in planned patient enrollment may result in increased costs and
prolonged clinical development. In addition, patients may withdraw from a
clinical trial for a variety of reasons. If we fail to accrue and maintain the
number of patients into one of our clinical trials for which the clinical trial
was designed, the statistical power of that clinical trial may be reduced which
would make it harder to demonstrate that the products being tested in such
clinical trial are safe and effective. Regulatory authorities, clinical investigators, institutional review boards,
data safety monitoring boards and the hospitals at which our clinical trials
are conducted all have the power to stop our clinical trials prior to
completion. If our studies are not completed, we would be unable to show the
safety and efficacy required to obtain marketing authorization for our
products. We may not be able to obtain marketing approvals for our products, which would
materially impair our ability to generate revenue. We are not able to market any of our products in the United States, Europe or
in any other jurisdiction without marketing approval from the FDA, the European
Commission, or any equivalent foreign regulatory agency. The regulatory process
to obtain marketing approval for a new drug or biologic takes many years and
requires the expenditure of substantial resources. This process can vary
substantially based on the type, complexity, novelty and indication of the
product candidate involved. In August 2001, the European Commission granted marketing authorization of
Replagal in the European Union, approximately one year after we submitted our
marketing authorization application, or MAA, to the European Agency for the
Evaluation of Medicinal Products, or EMEA, and approximately five years after
we filed our investigational new drug application, or IND, with the FDA. The
FDA never approved Replagal in the United States and, in January 2004, we
withdrew our BLA for Replagal. We are continuing to seek marketing approval for
Replagal in a number of other countries in the world. However, we may not
obtain approvals in one or more of these countries. We are currently conducting a pivotal clinical trial of I2S in 96 patients with
Hunter syndrome at nine sites around the world. If the results are positive, we
expect to submit applications for marketing approval in the United States and
in the European Union in the second half of 2005. However, even if we submit
such applications, the FDA, the European Commission and other regulatory
agencies to which we submit applications may not agree that our product is safe
and effective and may not approve our product. Although the European Commission has granted marketing approval of Dynepo in
the European Union, Dynepo has not been approved in the United States. In 2000,
Aventis Pharmaceuticals Inc. submitted a BLA to the FDA seeking marketing
authorization for Dynepo in the United States. The FDA did not accept the BLA
for filing, and requested that Aventis provide additional manufacturing data.
Aventis has not yet submitted the requested additional data to the FDA, and we
cannot predict whether or when Aventis will do so. There can be no assurance as to whether or when any of our applications for
marketing authorization relating to any of our products, including Replagal,
I2S, and Dynepo, or additional applications for marketing authorization that we
may make in the future as to these 23




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or other products, will be approved by the relevant regulatory authorities.
Among other things, we have had only limited experience in preparing
applications and obtaining regulatory approvals. If approval is granted, it may
be subject to limitations on the indicated uses for which the product may be
marketed or contain requirements for costly post-marketing testing and
surveillance to monitor safety or efficacy of the product. For example, there
are conditions associated with our European Union approval of Replagal,
including an obligation to conduct additional clinical trials and an obligation
to submit an annual assessment of Replagal for review by the Committee for
Proprietary Medicinal Products, or CPMP. If we do not complete these clinical
trials on a timely basis or the results of these trials are not satisfactory to
the CPMP, the European Commission may withdraw or suspend our Replagal
approval. If approval of an application to market a product is not granted on a
timely basis or at all, or we are unable to maintain our approval, our business
may be materially harmed. We may not be able to obtain orphan drug exclusivity for our products for the
treatment of rare genetic diseases. If our competitors are able to obtain
orphan drug exclusivity for their products, we may not be able to have our
competitive products approved by the applicable regulatory authority for a
significant period of time. Some jurisdictions, including the European Union and the United States, may
designate drugs for relatively small patient populations as orphan drugs.
Orphan drug designation must be requested before submitting an application for
marketing authorization. Orphan drug designation does not convey any advantage
in, or shorten the duration of, the regulatory review and approval process, but
does make the product eligible for orphan drug exclusivity and, in the United
States, certain tax credits. Generally, if a product with an orphan drug
designation subsequently receives the first marketing approval for the
indication for which it has such designation, the product is entitled to orphan
drug exclusivity. Orphan drug exclusivity means that another application to
market the same drug for the same indication may not be approved for a period
of up to 10 years in the European Union, and for a period of seven years in the
United States, except in limited circumstances set forth in the U.S. Food, Drug
and Cosmetic Act and its implementing regulations, which we refer to as the FDA
law. Obtaining orphan drug designations and orphan drug exclusivity for our
products for the treatment of rare genetic diseases may be critical to the
success of these products. Our competitors may obtain orphan drug exclusivity
for products competitive with our products before we do as Genzyme Corporation
did with its Fabrazyme product in the United States, as discussed below. Even
if we obtain orphan drug exclusivity for any of our potential products, we may
not be able to maintain it. For example, if a competitive product is shown to
be clinically superior to our product, any orphan drug exclusivity we have
obtained will not block the approval of such competitive product. In August 2001, the European Commission granted marketing authorization of
Replagal in the European Union. The European Commission also granted marketing
authorization of Genzyme Corporations Fabrazyme product in the European Union
in August 2001. In connection with these approvals, the European Commission
granted Replagal and Fabrazyme co-exclusive orphan drug status in the European
Union for up to 10 years. In April 2003, Genzyme received marketing authorization in the United States
for Fabrazyme. Because Fabrazyme had received orphan drug designation in the
United States, upon its marketing approval, Fabrazyme received orphan drug
exclusivity. Because Fabrazyme received marketing approval in the United States
before Replagal and received orphan drug exclusivity, the FDA may not approve
Replagal and Replagal will be excluded from the United States market for seven
years, until April 2010, unless we receive approval to market and sell Replagal
in the United States and we can demonstrate that Replagal satisfies the limited
criteria for exceptions set forth in the FDA law. In January 2004, we withdrew
our BLA for Replagal. We will not be able to market Replagal in the United
States unless we resubmit, and obtain the FDAs approval of, our BLA for
Replagal. In November 2001, our I2S product for the treatment of Hunter syndrome was
designated an orphan drug in the United States and in the European Union. If
our I2S product is the first such product to receive marketing approval for
Hunter syndrome, then our I2S product will be entitled to orphan drug
exclusivity and no other application to market the same drug for the same
indication may be approved, except in limited circumstances, for a period of up
to 10 years in the European Union and for a period of seven years in the United
States. If we are not able to maintain this orphan drug exclusivity, our
business may be adversely affected. If we fail to comply with the extensive regulatory requirements to which we and
our products are subject, our products could be subject to restrictions or
withdrawal from the market and we could be subject to penalties. The testing, manufacturing, labeling, advertising, promotion, export, and
marketing, among other things, of our products, both before and after approval,
are subject to extensive regulation by governmental authorities in the United
States, Europe and elsewhere throughout the world. Failure to comply with the
law administered by the FDA, the EMEA, or other governmental authorities could
result in any of the following:  delay in approving or refusal to approve a product;  product recall or seizure;  interruption of production; 24




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 operating restrictions;  warning letters;  injunctions;  criminal prosecutions; and  unanticipated expenditures. For example, the European Commission approved Replagal under exceptional
circumstances. Approval under exceptional circumstances means that the
European Commission accepted less-than-complete clinical data because it
determined that it would be impractical or unethical for the drug sponsor to
carry out full-scale pivotal clinical trials. The European Commission imposes
specific obligations on the drug sponsor when granting such approvals. These
obligations form part of the formal marketing authorization issued by the
European Commission and are reviewed by the CPMP at the intervals specified,
minimally on an annual basis. The annual review includes a reassessment of the
overall benefit/risk ratio of the product. If the drug sponsor does not fulfill
the specific obligations imposed in connection with approval, the European
Commission may vary, suspend or withdraw the marketing authorization for the
product. The European Commission required us as part of its post-approval
requirements for Replagal to conduct additional clinical trials of Replagal. If
we do not complete these clinical trials on a timely basis, the results of
these studies are not satisfactory to the CPMP or we otherwise fail to comply
with the conditions imposed on us pursuant to the approval under exceptional
circumstances, the European Commission could withdraw or suspend its approval
of Replagal. Because Replagal is currently our only commercial product, the
withdrawal or suspension of the European Commissions approval of Replagal
could materially adversely affect our business, results of operations and
financial condition. We are required to maintain pharmacovigilance systems for collecting and
reporting information concerning suspected adverse reactions to our products.
In response to pharmacovigilance reports, regulatory authorities may initiate
proceedings to revise the prescribing information for our products or to
suspend or revoke our marketing authorizations. Procedural safeguards are often
limited, and marketing authorizations can be suspended with little or no
advance notice. Both before and after approval of a product, quality control and manufacturing
procedures must conform to current good manufacturing practice regulations, or
GMP. Regulatory authorities, including the EMEA and the FDA, periodically
inspect manufacturing facilities to assess compliance with GMP. Accordingly, we
and our contract manufacturers will need to continue to expend time, monies,
and effort in the area of production and quality control to maintain GMP
compliance. In addition to regulations adopted by the EMEA, the FDA, and other foreign
regulatory authorities, we are also subject to regulation under the
Occupational Safety and Health Act, the Toxic Substances Control Act, the
Resource Conservation and Recovery Act, and other federal, state, and local
regulations. If we fail to obtain marketing authorizations in a timely manner, our costs
associated with clinical trials will increase. After completion of a clinical trial designed to show safety or effectiveness,
we often enroll patients taking our products in maintenance clinical trials in
which these patients continue to receive treatment with our products pending
approval for marketing authorization in the relevant jurisdiction. We receive
no payments for such treatment. The costs associated with maintaining
open-ended maintenance clinical trials can be significant. If we fail to obtain
marketing authorizations in a timely manner for the product being tested in
such trials, our costs associated with these maintenance clinical trials will
increase and we may continue to supply the product for use in clinical trials
without remuneration to us. Our research and development efforts may not result in products appropriate for
testing in human clinical trials. We expend significant resources on research and development and preclinical
studies of product candidates. However, these efforts may not result in the
development of products appropriate for testing in human clinical trials. For
example, our research may result in product candidates that are not expected to
be effective in treating diseases or may reveal safety concerns with respect to
product candidates. We may postpone or terminate research and development of a
product candidate or a program at any time for any reason such as the safety or
effectiveness of the potential product, allocation of resources or
unavailability of qualified research and development personnel. Adverse events in the field of gene therapy may impair our ability to enter
into collaborative arrangements for our gene therapy programs. In connection with our restructuring in the first quarter of 2003, we
terminated internal development of our gene therapy programs and 25




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now are seeking collaborators with which to continue to develop these programs.
Adverse events in the field of gene therapy, although not occurring in our
clinical trials, may impair our ability to generate value from our gene therapy
programs or to enter into collaborations for our programs. In particular, in
November 1999, a patient with a rare metabolic disorder died in a gene therapy
trial conducted at the University of Pennsylvania. In addition, in October
2002, a French boy developed a leukemia-like disease nearly three years after
participating in a gene therapy study as a baby. As a result of these and other
events, a number of gene therapy clinical trials have been terminated or
suspended in the United States and in other countries, and regulatory
authorities have grown increasingly concerned about the safety of gene therapy. Litigation and intellectual property risks We are a party to litigation with Kirin-Amgen, Inc. and Amgen Inc. involving
Dynepo which could preclude us from manufacturing or selling Dynepo in the
United Kingdom and the United States. In July 1999, we commenced legal proceedings with Aventis in the United Kingdom
against Kirin-Amgen, which sought a declaration that a U.K. patent held by
Kirin-Amgen will not be infringed by our activities relating to Dynepo and that
certain claims of Kirin-Amgens U.K. patent are invalid. In April 2001, the
High Court of Justice in the United Kingdom ruled that Dynepo infringed one of
four claims of the patent asserted by Kirin-Amgen. In July 2002, the Court of
Appeals in the United Kingdom reversed the High Court of Justice and ruled that
Dynepo did not infringe Kirin-Amgens patent. Kirin-Amgen petitioned the House
of Lords to hear an appeal from the decision of the Court of Appeals. The House
of Lords agreed to hear this appeal during the summer of 2004. Although
Kirin-Amgens U.K. patent expires in December 2004, if Kirin-Amgens appeal to
the House of Lords is successful, Kirin-Amgen will have the right to seek a
post-expiry injunction against Aventis and us to preclude us from manufacturing
or selling Dynepo in the United Kingdom for a period of time after the U.K.
patent expires equal to the period during which Kirin-Amgen alleges that we and
Aventis infringed the U.K. patent. In addition, in April 1997, Amgen commenced a patent infringement action
against us and Aventis in the United States District Court of Massachusetts. In
January 2001, the United States District Court of Massachusetts concluded that
Dynepo infringed eight of the 18 claims of five patents that Amgen had
asserted. Amgen did not seek and was not awarded monetary damages. In January 2003, the United States Court of Appeals for the Federal Circuit
issued a decision affirming in part and reversing in part the decision of the
United States District Court of Massachusetts and remanded the action to the
United States District Court of Massachusetts for further proceedings. In
particular, the United States Court of Appeals for the Federal Circuit:  upheld the United States District Court of Massachusetts determination
of invalidity of one of Amgens patents;  upheld the United States District Court of Massachusetts determination
that some claims of two other Amgen patents were infringed, but vacated
the United States District Court of Massachusetts determination that
those patents were not invalid; and  vacated the United States District Court of Massachusetts determination
that Dynepo infringed some claims of the two remaining Amgen patents, and
vacated the United States District Court of Massachusetts determination
that one of these patents was not invalid. As part of the United States Court of Appeals for the Federal Circuits ruling,
it remanded the case to the United States District Court of Massachusetts and
instructed it to reconsider the validity of Amgens patents in light of
potentially invalidating prior art. The United States District Court of
Massachusetts has concluded the remand proceedings and heard oral argument on
some of these issues in July 2003. We expect that the United States District
Court of Massachusetts will enter a decision on the remanded issues at some
point during the first half of 2004. The United States District Court of
Massachusetts also recently issued a decision upholding its earlier findings
that Amgen successfully rebutted the presumption of prosecution history
estoppel with respect to certain of its patents, and therefore, that we and
Aventis infringe such patents in light of recent Supreme Court precedents. On
remand, we and Aventis presented affirmative defenses with respect to such
patents. We, Amgen and Aventis all have the right to appeal the decision of the
United States District Court of Massachusetts to the United States Court of
Appeals for the Federal Circuit. We can provide no assurance as to the outcome of either litigation. If we and
Aventis are not successful in the Dynepo litigation, we and Aventis would be
precluded from making, using and selling Dynepo in the United States and/or in
the United Kingdom, as applicable. We are required to reimburse Aventis, which
controls the U.S. litigation and is paying the U.S. litigation expenses, for
50% of the expenses incurred in connection with the U.S. litigation from and
after March 26, 2004. Aventis is entitled to deduct up to 50% of any royalties
that Aventis may otherwise owe us with respect to the sale of Dynepo until
Aventis has recouped the full amount of our share of the U.S. litigation
expenses. We have the right to control the U.K. litigation and any other
litigation that might arise outside of the United States and are responsible
for all litigation expenses incurred in connection with such litigation from
and after March 26, 2004. 26




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We are a party to a shareholder lawsuit and a derivative action regarding the
adequacy of our public disclosure which could have a material adverse affect on
our business, results of operations and financial condition. In January and February 2003, various parties filed purported class action
lawsuits against us and Richard Selden, our former Chief Executive Officer, in
the United States District Court for the District of Massachusetts. The
complaints generally allege securities fraud during the period from January
2001 through January 2003. Each of the complaints asserts claims under Section
10(b) of the Securities Exchange Act of 1934, Rule 10b-5 promulgated
thereunder, and Section 20(a) of the Exchange Act, and alleges that we and our
officers made false and misleading statements and failed to disclose material
information concerning the status and progress for obtaining United States
marketing approval of our Replagal product to treat Fabry disease during that
period. In March 2003, various plaintiffs filed motions to consolidate, to appoint lead
plaintiff, and to approve plaintiffs selections of lead plaintiffs counsel.
In April 2003, various plaintiffs filed a Joint Stipulation and Proposed Order
of Lead Plaintiff Applicants to Consolidate Actions, To Appoint Lead Plaintiffs
and to Approve Lead Plaintiffs Selection of Lead Counsel, Executive Committee
and Liaison Counsel. In April 2003, the Court endorsed the Proposed Order,
thereby consolidating the various matters under one matter: In re Transkaryotic
Therapies, Inc., Securities Litigation, C.A. No. 03-10165-RWZ. In July 2003, the plaintiffs filed a Consolidated and Amended Class Action
Complaint, which we refer to as the Amended Complaint, against us; Dr. Selden;
Daniel Geffken, our former Chief Financial Officer; Walter Gilbert, Jonathan S.
Leff, Rodman W. Moorhead, III, and Wayne P. Yetter, members of our board of
directors; William R. Miller and James E. Thomas, former members of our board
of directors; and SG Cowen Securities Corporation, Deutsche Bank Securities
Inc., Pacific Growth Equities, Inc. and Leerink Swann & Company, underwriters
of our common stock in prior public offerings. The Amended Complaint alleges securities fraud during the period from January
4, 2001 through January 10, 2003. The Amended Complaint alleges that the
defendants made false and misleading statements and failed to disclose material
information concerning the status and progress for obtaining United States
marketing approval of Replagal during that period. The Amended Complaint
asserts claims against each of the defendants under Section 11 of the
Securities Act of 1933 and against Dr. Selden under Section 15 of the
Securities Act; against SG Cowen Securities Corporation, Deutsche Bank
Securities, Pacific Growth Equities, Inc., and Leerink Swann & Company under
Section 12(a)(2) of the Securities Act; against Dr. Selden and us under Section
10(b) of the Exchange Act and Rule 10b-5 promulgated thereunder; and against
Dr. Selden under Section 20(a) of the Exchange Act. The plaintiffs seek
equitable and monetary relief, an unspecified amount of damages, with interest,
and attorneys fees and costs. In September 2003, we filed a motion to dismiss the Amended Complaint. A
hearing of the motion occurred in December 2003. A class has not been
certified, and the court has not made any decision on the motion. In April 2003, South Shore Gastrointerology UA 6/6/1980 FBO Harold Jacob, and
Nancy R. Jacob Ttee filed a Shareholder Derivative Complaint against Dr.
Selden; against the following members of our board of directors: Jonathan S.
Leff, Walter Gilbert, Wayne P. Yetter, Rodman W. Moorhead III; against the
following former members of our board of directors: James E. Thomas, and
William Miller; and against us as nominal defendant, in Middlesex Superior
Court in the Commonwealth of Massachusetts, Civil Action No. 03-1669. On May
29, 2003, the parties moved to transfer venue to the Business Litigation
Session in Suffolk Superior Court in the Commonwealth of Massachusetts. The
parties motion was allowed, and in June 2003 the matter was accepted into the
Business Litigation Session as Civil Action No. 03-02630-BLS. The complaint alleges that the individual defendants breached fiduciary duties
owed to us and our shareholders by disseminating materially false and
misleading statements to the market and causing or allowing us to conduct our
business in an unsafe, imprudent and unlawful manner. The complaint purports to
assert derivative claims against the individual defendants for breach of
fiduciary duty, and to assert a claim for contribution and indemnification on
behalf of us for any liability we incur as a result of the individual
defendants alleged misconduct. The complaint seeks declaratory, equitable and
monetary relief, an unspecified amount of damages, with interest, and
attorneys fees and costs. In August 2003, the plaintiff filed its Verified
Amended Derivative Complaint, which we refer to as the Amended Derivative
Complaint. The Amended Derivative Complaint alleges that the individual
defendants breached fiduciary duties owed to us and our stockholders by causing
us to issue materially false and misleading statements to the public, by
signing our Form 10-Ks for the years 2000 and 2001 and by signing a
registration statement. The Amended Derivative Complaint also alleges that
defendant Dr. Selden sold our stock while in possession of material non-public
information. The plaintiffs seek declaratory, equitable and monetary relief, an
unspecified amount of damages, with interest, and attorneys fees and costs. In September 2003, we served a motion to dismiss the Amended Derivative
Complaint. A hearing of the motion was held in January 2004. In May 2004, the Court granted the Companys motion to dismiss. The plaintiffs may appeal this ruling. As of March 31, 2004, we had spent approximately $1.1 million related to these
lawsuits. We expect that the costs related to these suits will be significant.
We can provide no assurance as to the outcome of any of these suits. If we are
not successful in defending these actions, our business, results of operations
and financial condition could be materially adversely affected. In addition,
even if we are successful, the defense of these actions may divert the
attention of our management and other resources that would otherwise be 27




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engaged in running our business. The SEC is investigating us regarding our public disclosures and filings, as
well as transactions in our securities, which could have a material adverse
effect on our business, results of operations and financial condition. In May 2003, we received a copy of a formal order of investigation by the SEC.
The order of investigation relates to our disclosures and public filings with
regard to Replagal and the status of the FDAs approval process for Replagal,
as well as transactions in our securities. We are cooperating fully and will
continue to cooperate fully with the SEC in the investigation. As of March 31,
2004, we had spent approximately $1.4 million related to this matter. If this investigation results in a determination that we have failed to
properly disclose information relating to Replagal and the status of the FDAs
approval process for Replagal or that there were improper transactions in our
securities, we could be subject to substantial fines or penalties and other
sanctions. An adverse determination could have a material adverse effect on our
business, results of operations and financial condition. However, at this time,
we cannot accurately predict the outcome of this proceeding. In addition, even
if we are successful, this investigation may divert the attention of our
management and other resources that would otherwise be engaged in running our
business. We may become involved in additional and expensive patent litigation or other
proceedings, which could result in our incurring substantial costs and expenses
or substantial liability for damages or require us to stop our development and
commercialization efforts. The biotechnology industry has been characterized by significant litigation,
and other proceedings regarding patents, patent applications, and other
intellectual property rights. We may become a party to additional patent
litigation beyond the Amgen litigation described above and to other proceedings
with respect to our products and technologies. An adverse outcome in any patent litigation or other proceeding involving
patents could subject us to significant liabilities to third parties and
require us to cease using the technology or product that is at issue or to
license the technology or product from third parties. We may not be able to
obtain any required licenses on commercially acceptable terms, or at all. The cost to us of any patent litigation or other proceeding, even if resolved
in our favor, could be substantial. In addition, any such litigation or
proceeding will divert managements attention and resources. Some of our
competitors may be able to sustain these costs more effectively than we can
because of their substantially greater financial resources. Uncertainties
resulting from the initiation and continuation of patent litigation or other
proceedings could have a material adverse effect on our ability to develop,
manufacture, and market products, form collaborations, and compete in the
marketplace. If we are unable to obtain and maintain patent protection for our discoveries,
the value of our technology and products may be adversely affected. Our success will depend in large part on our ability to obtain and maintain
patent protection for our processes and products in the United States and other
countries. The patent situation in the field of biotechnology generally is
highly uncertain and involves complex legal, scientific and factual questions.
We may not be issued patents relating to our technology or products. Even if
issued, patents may be challenged, invalidated, or circumvented, which could
limit our ability to stop competitors from marketing similar products or limit
the length of term of patent protection we may have for our products. Changes
in patent laws or in interpretations of patent laws in the United States and
other countries may diminish the value of our intellectual property or narrow
the scope of our patent protection. Our patents also may not afford us protection against competitors with similar
technology. Because some patent applications in the United States and many
foreign jurisdictions are typically not published until 18 months after filing
or are maintained in secrecy until patents issue from those patent
applications, third parties may have filed or maintained patent applications
for technology used by us or covered by our pending patent applications without
our being aware of these applications. For this reason, we cannot be certain
that we were the first to make the inventions claimed in issued patents or
pending patent applications, or that we were the first to file for protection
of the inventions set forth in these patent applications. As a result, third
parties could assert claims against us concerning our gene activation or other
technology. Our overall patent strategy with respect to our gene activation technology and
our protein products made using our gene activation technology is to attempt to
obtain patent coverage for gene activation of the gene that encodes the
product, the composition of matter of the product, the method of making the
product, cells or cell lines capable of expressing the product, and the genetic
constructs used to obtain the product. We have been unable to obtain patent
claims in all categories with respect to all of our Gene-Activated protein
products. Nonetheless, while our patent portfolio may afford us protection
against competitors with similar technology and competitors which attempt to
make products in human cell or cell lines, it may not afford us protection
against all competitors, such as those who make the same products in mouse,
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The expiration dates for the patents and patent applications covering our
principal products are as follows:  ReplagalThe principal issued patents and patents that may issue from
pending patent applications covering Replagal expire or will expire in the
United States in 2017 and in Europe at various dates from 2012 to 2017.  I2SThe principal issued patents and patents that may issue from pending
patent applications covering I2S expire or will expire in the United
States at various dates from 2011 to 2016. There are no European patents
or pending patent applications covering I2S.  GA-GCBThe principal issued patents and patents that may issue from
pending patent applications covering GA-GCB expire or will expire in the
United States at various dates from 2014 to 2017 and in Europe in 2012.  DynepoThe principal issued patents and patents that may issue from
pending patent applications covering Dynepo expire or will expire in the
United States at various dates from 2011 to 2018 and in Europe in 2012. Third parties may own or control patents or patent applications and require us
to seek licenses, which would increase our development and commercialization
costs, or prevent us from developing or marketing our products or technologies. We may not hold proprietary rights to certain product patents, process patents,
and use patents related to our products or their methods of manufacture. In
some cases, these patents may be owned or controlled by third parties.
Therefore, in some cases, in order to develop, manufacture, sell or import some
of our existing and proposed products or processes, we may choose to seek, or
be required to seek, licenses under third party patents or those patents that
might issue from patent applications. In such event, we would be required to
pay license fees or royalties or both to the licensor. If licenses are not
available to us on acceptable terms, we or our collaborators may not be able to
develop, manufacture, sell, use or import the affected products or processes. For example, we are aware of third party patents and patent applications that
relate to gene activation. We believe that our gene activation technology does
not infringe any third party patents that we believe to be valid. We use our
gene activation technology to manufacture Replagal, Dynepo, GA-GCB and other
products. If the use of our gene activation technology were found to infringe a
valid third party patent, we could be precluded from manufacturing and selling
such products and our business, results of operations and financial condition
would be materially adversely affected. If we are unable to protect the confidentiality of our proprietary information
and know-how, the value of our technology and products will be adversely
affected. We rely upon unpatented proprietary technology, processes, and know-how. We
seek to protect this information in part by confidentiality agreements with our
employees, consultants, and other third party contractors. These agreements may
be breached, and we may not have adequate remedies for any such breach. In
addition, our trade secrets may otherwise become known or be independently
developed by competitors. If we fail to comply with our obligations under the agreements under which we
license commercialization rights to products or technology from third parties,
we could lose license rights. We are a party to over 20 patent licenses under which we have acquired rights
to proprietary technology of third parties, including licenses to patents
related to I2S and Dynepo, and expect to enter into additional patent licenses
in the future. These licenses impose various commercialization, sublicensing,
royalty, insurance, and other obligations on us. If we fail to comply with
these obligations, the licensor may have the right to terminate the license and
we could lose our license to use the acquired rights. If these rights are lost,
we may not be able to market products that were covered by the license. Business risks Our revenue from product sales is dependent on the commercial success of
Replagal. Replagal is our only commercial product. We expect that Replagal will account
for all of our product sales until at least the fourth quarter of 2005. The
commercial success of Replagal will depend on its acceptance by physicians,
patients and other key decision-makers for the treatment of Fabry disease. The
commercial success of Replagal will also depend in part upon Replagal receiving
marketing approval in Japan and other countries. We have ceased our efforts to
seek the approval of Replagal in the United States. If Replagal is not
commercially successful, our business, results of operations and financial
condition will be materially adversely affected. Our revenue from sales of Replagal and our cash held by TKT Europe are subject
to foreign currency fluctuations. 29




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We have exposure to currency risk for Replagal sales in Europe.
Country-by-country pricing of Replagal was initially established as the local
currency equivalent of between approximately $165,000 and $175,000 per patient
per year for an average patient weighing 70 kilograms. The price generally
remains fixed in the local currencies and varies in United States dollars with
exchange rate fluctuations. Since the approval of Replagal in August 2001, the
United States dollar has weakened substantially versus most European
currencies, including the Euro, which has resulted in increased revenues for us
from sales of Replagal. If the United States dollar were to strengthen versus
these currencies, this currency fluctuation would adversely impact our Replagal
product sales. Foreign currency fluctuations favorably contributed $2.4 million
to product sales for the three months ended March 31, 2004 as compared to first
quarter of 2003 and $9.4 million to product sales for the year ended December
31, 2003 as compared to the same period of 2002. We also have exposure to currency risk for cash and cash equivalents held by
TKT Europe, which are primarily denominated in Swedish Krona, British Pound and
Euro. Any change in the value of the U.S. dollar as compared to these foreign
currencies may have an adverse effect on our liquidity. For example, a
hypothetical 10 percent strengthening of the U.S. dollar relative to these
foreign currencies would result in an approximate $6.8 million decrease in our
cash and marketable securities held by TKT Europe as of March 31, 2004. The continuity of our sales of Replagal in Europe may be affected by our
expected purchase of the holdings of the minority stockholders of TKT Europe. In April 2000, we established an 80%-owned subsidiary, TKT Europe, for the
purpose of marketing, selling and distributing Replagal in Europe. Under the
stockholders agreement for TKT Europe, we agreed that the holders of the
remaining 20% interest in TKT Europe would, with specified exceptions, manage
the day-to-day operations of TKT Europe. As a result, our ability to
successfully market and sell Replagal in Europe has been dependent on the
efforts of the minority stockholders of TKT Europe. Under the stockholders agreement for TKT Europe, we are entitled to purchase
the minority stockholders 20% ownership interest in TKT Europe beginning in
September 2004 for a price determined in accordance with a formula. Should we
not exercise that right, the minority stockholders of TKT Europe can require us
to purchase the minority stockholders ownership interest sixty days
thereafter. We currently expect that we will purchase the minority
stockholders interest in TKT Europe for between $55 million and $65 million
based on our current estimates for sales and expenses. If we purchase the minority stockholders interest in TKT Europe or if the
minority stockholders exercise their contractual right to require us to
purchase their interest, our ability to successfully market and sell Replagal
in Europe thereafter will depend in part on our ability to integrate the
functions of TKT Europe into our infrastructure. In addition, if we cannot
retain existing marketing and sales personnel of TKT Europe, it is likely that
the current relationships that TKT Europe maintains with patients, physicians
and other key decision-makers for the treatment of Fabry disease will be
affected, which could adversely affect our business and results of operations
in Europe, including our sales of Replagal, and could result in the loss of
sales and market share for Replagal in Europe. We face significant competition, which may result in others discovering,
developing or commercializing products before, or more successfully, than we
do. The biotechnology industry is highly competitive and characterized by rapid and
significant technological change. Our competitors include pharmaceutical
companies, biotechnology firms, universities, and other research institutions.
Many of these competitors have substantially greater financial and other
resources than we do and are conducting extensive research and development
activities on technologies and products similar to, or competitive with, ours. We may be unable to develop technologies and products that are more clinically
efficacious or cost-effective than products developed by our competitors. Even
if we obtain marketing approval for our product candidates, many of our
competitors have more extensive and established sales, marketing, and
distribution capabilities than we do. Litigation with third parties, such as
our litigation with Amgen, could delay our time to market or preclude us from
reaching the market for certain products and enable our competitors to more
quickly and effectively penetrate certain markets. Therapeutics for the treatment of rare genetic diseases We believe that the primary competition with respect to our products for the
treatment of rare genetic diseases is from biotechnology and smaller
pharmaceutical companies. Competitors include Actelion Ltd., BioMarin
Pharmaceutical Inc., and Genzyme. The markets for some of the potential
therapeutics for rare genetic diseases caused by protein deficiencies are quite
small. As a result, if competitive products exist, we may not be able to
successfully commercialize our products. Our primary competition with respect to Replagal is Genzyme. Replagal and
Fabrazyme were each granted marketing authorization in the European Union and
were also granted co-exclusive orphan drug status in the European Union for up
to 10 years. Fabrazyme has 30




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received marketing authorization and orphan drug exclusivity in the United
States. We believe that our primary competition with respect to our GA-GCB product for
the treatment of Gaucher disease will be Genzymes product for the treatment of
Gaucher disease, Cerezyme. Gene-Activated versions of proteins that would compete with currently-marketed
proteins We have developed several Gene-Activated protein products that would compete
with proteins that are currently being marketed by third parties. For instance,
in the case of Dynepo, competing products are marketed by Amgen, Johnson &
Johnson, F. Hoffmann-La Roche Ltd. (Boehringer Mannheim GmbH), Sankyo Company
Ltd., Chugai Pharmaceutical Co., Ltd., and the pharmaceutical division of Kirin
Brewery Co., Ltd. in Japan. Additional competitors to Dynepo may emerge
following the expiration of Amgens European patents in December 2004. Many of the products against which our Gene-Activated protein products, such as
Dynepo and GA-GCB, would compete have well-known brand names, have been
promoted extensively, and have achieved market acceptance by third party
payors, hospitals, physicians, and patients. In addition, many of the companies
that produce these protein products have patents covering techniques used to
produce these products, which have often served as effective barriers to entry
in the therapeutic proteins market. As with Amgen and its erythropoietin
product, these companies may seek to block our entry into the market by
asserting that our Gene-Activated protein products infringe their patents. Many
of these companies are also seeking to develop and commercialize new or
potentially improved versions of their proteins. Gene therapy Our gene therapy system will have to compete with other gene therapy systems,
as well as with conventional methods of treating the disease and conditions
targeted. Although no gene therapy product is currently marketed, a number of
companies, including major biotechnology companies, pharmaceutical companies
and development stage companies, are actively involved in this field. The commercial success of our products will depend on the degree that the
market is receptive to our products upon introduction. The commercial success of any of our products for which we obtain marketing
approval from the European Commission, the FDA, and other regulatory
authorities will depend upon their acceptance by patients, the medical
community and third party payors as clinically effective, safe and
cost-effective. It may be difficult for us to achieve market acceptance of our
products. Other factors that we believe will materially affect market acceptance of our
products include:  the timing of the receipt of marketing approvals;  the countries in which such approvals are obtained; and  the safety, efficacy, convenience, and cost-effectiveness of the product
as compared to competitive products. If we cannot achieve market acceptance for our products, our business, results
of operations and financial condition will be adversely affected. We have limited manufacturing experience and may not be able to develop the
experience and capabilities needed to manufacture our products in compliance
with regulatory requirements. If we cannot develop this experience or
capabilities, we may not be able to manufacture our products, the manufacture
of our products may be subject to significant delays or we may incur
significant costs. The manufacture of proteins is complicated and technical. We have limited
manufacturing experience. In order to continue to develop products, apply for
regulatory approvals, and commercialize our products, we will need to develop,
contract for, or otherwise arrange for the necessary manufacturing
capabilities. We have manufactured, and plan to continue in the future to
manufacture, the bulk drug substance for Replagal, I2S and GA-GCB for
preclinical testing, clinical trials, and commercial sale. We intend to engage
third party contract manufacturers to manufacture Dynepo for us. Any manufacturing of our products must comply with GMP as required by the
countries in which we intend to sell our products. Before approving an
application for marketing authorization for a product, the FDA, the European
Commission, or any other equivalent foreign regulatory agency will inspect the
facilities at which the product is manufactured. If we or our third party
manufacturers do not comply with applicable GMP, such regulatory agency may
refuse to approve our application for marketing authorization. Once the
regulatory agency approves a product, we or our third party manufacturers must
continue to comply with GMP. If we or our third party manufacturers fail to
maintain compliance with GMP, adverse consequences can result, including 31




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suspension or withdrawal of an approved product from the market, operating
restrictions, and the imposition of civil and criminal penalties. We are developing new manufacturing processes to produce bulk drug substance
for Replagal. In the European Union, we will need to obtain regulatory approval
of an amendment to our MAA describing these processes for Replagal before we
can sell Replagal manufactured using these processes. If we cannot obtain this
regulatory approval, we will not be able to sell Replagal manufactured using
these processes. In some of our manufacturing processes, we use bovine-derived serum sourced
from Canada and the United States. The discovery of cattle in both Canada and
the United States with bovine spongiform encephalopathy, or mad cow disease,
could cause the regulatory agencies in some countries to impose restrictions on
our products, or prohibit us from using our products at all in such countries. We are incurring significant costs to expand and renovate our manufacturing
facility. Any delays in completing the expansion and renovation of our facility
and bringing the facility into compliance with GMP could adversely affect our
ability to supply the bulk drug substance needed to manufacture our products
other than Dynepo. We are investing substantial funds to expand the capacity of our manufacturing
facility in Cambridge, Massachusetts and to configure the facility for the
production at a commercial scale of additional products. In anticipation of
this expansion and renovation, in the third quarter of 2003, we ceased all
manufacturing operations at our manufacturing facility, including the
manufacture of Replagal. We expect to complete this expansion and renovation in
the first half of 2004 and recommence manufacturing operations in the second
half of 2004. Following completion of this expansion and renovation, our
manufacturing facility will have to comply with GMP before we can ship bulk
drug substance made at our manufacturing facility for commercial sale and
clinical trials. If we are unable to successfully complete this expansion and
renovation in a timely manner or to bring the facility into compliance with
GMP, our ability to supply our products for commercial sale and clinical use,
including Replagal, I2S and GA-GCB, could be interrupted and our sales of
Replagal and the timing of our I2S or GA-GCB clinical trials could be adversely
affected. We depend on third party contract manufacturers for various aspects of the
manufacture of Replagal, I2S and GA-GCB, including the preparation and
packaging of TKT-manufactured bulk drug substance into finished product, and
plan to depend entirely on third party contract manufacturers for the
manufacture of Dynepo. If these manufacturers fail to meet our requirements or
applicable regulatory requirements, our product development and
commercialization efforts may be materially harmed. To the extent that we are a party to manufacturing arrangements with third
parties, we are dependent upon these third parties to perform their obligations
in a timely manner and in accordance with applicable government regulations.
For instance, other than with respect to the manufacturing of the bulk drug
substance for Replagal, I2S, and GA-GCB, we rely on contract manufacturing
arrangements with third parties for all aspects of the manufacture of our
products, including the preparation and packaging of TKT-manufactured bulk drug
substance into finished product. Each of these manufacturing arrangements
relates to only some aspects of the manufacturing process. In the event that
any one of these manufacturers fails to or is unable to comply with its
obligations under its manufacturing, agreement with us, and if the
manufacturers failure materially delays the ultimate production of Replagal,
I2S, or GA-GCB or adversely affects our inventory levels, our sales of Replagal
or the timing of our I2S or GA-GCB clinical trials could be adversely affected. Before we can market and sell Dynepo in the European Union, we will need to
establish manufacturing capabilities for Dynepo outside of the United States.
Specifically, we will need to enter into arrangements with contract
manufacturers, work with the contract manufacturers to set up and validate
manufacturing processes and obtain the approval from the European Commission of
an amendment to the MAA for Dynepo reflecting the new manufacturing sites. If
we cannot establish contract manufacturing arrangements on favorable terms or
at all, successfully set up and validate manufacturing processes or obtain the
approval of the European Commission, we will not be able to sell Dynepo in the
European Union when planned, which could result in Dynepo being subject to
additional competition and which would adversely affect our cash resources. The value of the inventory under the control of our third party contract
manufacturers far exceeds the amount of liability such third parties are
willing to assume for their negligence. In the event that inventory in the
possession of one of our third party manufacturers is damaged, we could face
significant financial losses and we could also experience an interruption in
supply which could have a significant adverse affect on our sales. There are a limited number of third party manufacturers capable of
manufacturing our protein products with a limited amount of production
capacity. As a result, we may experience difficulty in obtaining adequate
manufacturing capacity for our needs. If we are unable to obtain or maintain
contract manufacturing of our products, or to do so on commercially reasonable
terms, we may not be able to complete development of our products or market
them. If we fail to manage our inventory correctly, or our inventory is destroyed,
damaged or expires, we could experience supply shortages and significant costs
to build inventory or a significant build-up of high-cost products and raw
materials, which could 32




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cause us to experience cash flow difficulties as well as financial losses. Manufacture of proteins, including our products and potential products, is
expensive and requires lengthy production cycle times. We build inventory of
both bulk drug substance and of finished product in order to ensure the
adequate supply to patients of our products and potential products, including
Replagal and I2S. Accordingly, we have significant capital invested in
inventory because of the high cost of manufacturing protein products, including
Replagal and I2S. In the event that any of our facilities containing inventory
are damaged, the inventory at the facility could be destroyed or damaged. We
may not be able to produce or have produced replacement inventory on a timely
basis or at all. We also have limited experience in managing our supply for
Replagal and our other potential products. If we fail to keep an adequate
inventory of our products, it is possible that patients could miss treatments,
which could have an adverse effect on our ability to sell our products and on
our clinical trials. Conversely, if we are unable to sell our high-cost
inventory in a timely manner, or if our high-cost inventory were to be
destroyed or expire, we could experience cash flow difficulties as well as
financial losses. Some of the raw materials used to manufacture our products are expensive and
are available from a small number of suppliers. If we fail to keep an adequate
inventory of our raw materials, it is possible that we would be unable to
manufacture our products in a timely manner. Conversely, if we are unable to
use our high-cost raw materials, or if our high-cost raw materials were to be
destroyed or expire, we could experience cash flow difficulties as well as
financial losses. If we fail to obtain reimbursement, or an adequate level of reimbursement, by
third party payors in a timely manner for our products, or if we are unable to
collect payment in a timely manner, we may not have commercially viable markets
for our products. In certain countries, particularly the countries of the European Union, the
pricing of prescription pharmaceuticals and the level of reimbursement are
subject to governmental control. In some countries, it can take an extended
period of time to establish and obtain reimbursement, and reimbursement
approval may be required at the individual patient level, which can lead to
further delays. In addition, in some countries such as Italy, Spain and
Belgium, it can take an extended period of time to collect payment even after
reimbursement has been established. In the United States and elsewhere, the availability of reimbursement by
governmental and other third party payors affects the market for any
pharmaceutical product. These third party payors continually attempt to contain
or reduce the costs of health care by challenging the prices charged for
medical products and services. For example, in Germany, the reimbursement
authority unilaterally reduced the price that it would reimburse for
pharmaceutical products, including Replagal, by six percent in 2003 and an
additional 10 percent in 2004. Governmental and reimbursement authorities or
third party payors in other countries may attempt to control costs by limiting
access to pharmaceutical products such as Replagal and the other products we
are developing or by narrowing the class of patients for which a pharmaceutical
product such as Replagal or the other products we are developing may be
prescribed. If we are not able to obtain pricing and reimbursement at
satisfactory levels for our products that receive marketing approval, our
revenues and results of operations will be adversely affected, possibly
materially. We expect that the prices for many of our products, when commercialized,
including in particular our products for the treatment of rare genetic
diseases, may be high compared to other pharmaceutical products. For example,
we have established pricing and reimbursement for substantially all patients
receiving Replagal in the European Union. Country-by-country pricing was
initially established as the local currency equivalent of between approximately
$165,000 and $175,000 per patient per year for an average patient weighing 70
kilograms. The price generally remains fixed in the local currencies and varies
in United States dollars with exchange rate fluctuations. We may encounter
particular difficulty in obtaining satisfactory pricing and reimbursement for
products for which we seek a high price. We also may experience pricing pressure with respect to Replagal and other
products for which we may obtain marketing approval due to the trend toward
managed health care, the increasing influence of health maintenance
organizations and legislative proposals. We may not be able to sell our
products profitably if reimbursement is unavailable or is limited in scope or
amount. We have limited sales and marketing experience and capabilities and will need
to develop this expertise or depend on third parties to successfully sell and
market our products on our behalf to generate revenue. Except for TKT Europe with respect to the marketing and selling of Replagal, we
have limited sales and marketing experience and capabilities, and limited
resources to devote to sales and marketing activities. In order to market our
products, including Replagal and Dynepo, we will need to develop this
experience and these capabilities or rely upon third parties to perform these
functions. If we rely on third parties to sell, market, or distribute our
products, our success will be dependent upon the efforts of these third parties
in performing these functions. In many instances, we may have little or no
control over the activities of these third parties in selling, marketing, and
distributing our products. If we choose to conduct these activities directly,
as we plan to do with respect to some of our potential products and with
Replagal following our expected purchase of the minority stockholders
interests in TKT Europe, we may not be able to recruit and maintain sales and
marketing personnel, which would adversely affect our sales efforts in Europe. 33




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Competition for technical, commercial and administrative personnel is intense
in our industry and we may not be able to sustain our operations or grow if we
are unable to attract and retain qualified personnel. While we do not feel that any single individual is indispensable, our success
is highly dependent on the retention of principal members of our technical,
commercial, and administrative staff. Our future growth will require hiring a significant number of qualified
technical, commercial and administrative personnel. Accordingly, recruiting and
retaining such personnel in the future will be critical to our success. There
is intense competition from other companies and research and academic
institutions for qualified personnel in the areas of our activities. If we are
not able to continue to attract and retain, on acceptable terms, the qualified
personnel necessary for the continued development of our business, we may not
be able to sustain our operations or grow. We depend on our collaborators to develop, conduct clinical trials of, obtain
regulatory approvals for, and manufacture, distribute, market and sell products
on our behalf and their efforts may not be scientifically or commercially
successful. We are parties to collaborative agreements with third parties relating to
certain of our principal products. We are relying on Genzyme to develop and
commercialize I2S in Japan and certain other countries in Asia; on Aventis to
develop, obtain regulatory approvals for, and manufacture, market, and sell
Dynepo in the United States; and Sumitomo to develop and commercialize Replagal
in Japan, Korea, China and Taiwan. We also use third party distributors to
distribute Replagal in many areas of the world including Australia, Canada,
Europe, and Israel. Our collaborators may not devote the resources necessary or
may otherwise be unable or unwilling to complete development and
commercialization of these potential products. Our existing collaborations are
subject to termination without cause on short notice under specified
circumstances. In some cases, we may not receive payments contemplated in the
agreements with our collaborators if our collaborators fail to achieve certain
regulatory and commercial milestones. Our existing collaborations and any future collaborative arrangements with
third parties may not be scientifically or commercially successful. Factors
that may affect the success of our collaborations include the following:  reductions in marketing or sales efforts or a discontinuation of
marketing or sales of our products by our collaborators would reduce our
revenues;  under our collaboration agreements, we cannot conduct specified types of
research and development and marketing and sales activities in the field
that is the subject of the collaboration. These agreements have the effect
of limiting the areas of research and development that we may pursue,
either alone or in cooperation with third parties;  our collaborators may underfund or not commit sufficient resources to
the testing, marketing, distribution or other development of our products;  our collaborators may be pursuing alternative technologies or developing
alternative products, either on their own or in collaboration with others,
that may be competitive with the product as to which they are
collaborating with us or that could affect our collaborators commitment
to the collaboration with us;  our collaborators may not properly maintain or defend our intellectual
property rights or they may utilize our proprietary information in such a
way as to invite litigation that could jeopardize or invalidate our
proprietary information or expose us to potential liability;  our collaborators may terminate their collaborations with us, as Aventis
has done with respect to our GA-GCSF product, which could make it
difficult for us to attract new collaborators or adversely affect the
perception of us in the business and financial communities; and  our collaborators may pursue higher priority programs or change the
focus of their development programs, which could affect the collaborators
commitment to us. If third parties on whom we rely for clinical trials do not perform as
contractually required or as we expect, we may not be able to obtain regulatory
approval for or commercialize our product candidates, and our business may
suffer. 34




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We do not have the ability to independently conduct the clinical trials
required to obtain regulatory approval for our products. We depend on
independent clinical investigators, contract research organizations and other
third party service providers to conduct the clinical trials of our product
candidates and expect to continue to do so. Although we rely heavily on these
parties for successful execution of our clinical trials, we do not control many
aspects of their activities. For example, the investigators are not our
employees. However, we are responsible for ensuring that each of our clinical
trials is conducted in accordance with the general investigational plan and
protocols for the trial. Third parties may not complete activities on schedule,
or may not conduct our clinical trials in accordance with regulatory
requirements or our stated protocols. The failure of these third parties to
carry out their obligations could delay or prevent the development, approval
and commercialization of our product candidates. A significant portion of our revenues are concentrated among a limited number
of significant customers. The loss of a significant customer could lower our
revenues and adversely affect our business, results of operations and financial
condition. We have three significant customers who accounted for 18%, 12% and 12%,
respectively, of our product sales in 2003. The same customers accounted for
8%, 6% and 22% of our product sales in 2002. The loss of any significant
customer may significantly lower our revenues and adversely affect our
business, results of operations and financial conditions. We may be exposed to product liability claims and may not be able to obtain
adequate product liability insurance. If we cannot successfully defend
ourselves against such claims, we may incur substantial liabilities and may be
required to limit commercialization of our products. Our business exposes us to the risk of product liability claims that is
inherent in the manufacturing, testing, and marketing of human therapeutic
products. We maintain clinical trial liability insurance and product liability
insurance in amounts that we believe to be reasonable. This insurance is
subject to deductibles and coverage limitations. We may not be able to obtain
additional insurance or maintain insurance on acceptable terms or at all.
Moreover, any insurance that we do obtain may not provide adequate protection
against potential liabilities. If we are unable to obtain insurance at
acceptable cost or otherwise protect against potential product liability
claims, we will be exposed to significant liabilities, which may materially and
adversely affect our business and financial position. These liabilities could
prevent or interfere with our product commercialization efforts. 35




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ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK The Company maintains its investment portfolio consistent with its Investment
Policy, which has been approved by the Board of Directors. The Companys
investment portfolio consists of investments only in U.S. government and agency
obligations. The Companys investments are also subject to interest rate risk
and will decrease in value if market interest rates increase. However, due to
the relatively short duration of the Companys investments, interest rate risk
is mitigated. The Company does not own derivative financial instruments in its
investment portfolio. Accordingly, the Company does not believe that there is any material market
risk exposure with respect to derivative or other financial instruments which
would require disclosure under this item. As of March 31, 2004, the Company did not have any off-balance sheet
arrangements. The Company has exposure to currency risk for Replagal sales in Europe. Pricing
was initially established as the local currency equivalent of an average annual
per patient price of approximately $165,000. The price remains fixed in the
local currencies and varies in U.S. dollars with exchange rate fluctuations.
Foreign currency fluctuations favorably contributed $2,400,000 to product sales
for the three months ended March 31, 2004 as compared to the same period of
2003. 
 ITEM 4. CONTROLS AND PROCEDURES. The Companys management, with the participation of the Companys President and
Chief Executive Officer and its Vice President, Finance and Chief Financial
Officer, evaluated the effectiveness of the Companys disclosure controls and
procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act)
as of March 31, 2004. Based on this evaluation, the Companys President and
Chief Executive Officer and its Vice President, Finance and Chief Financial
Officer concluded that, as of March 31, 2004, the Companys disclosure controls
and procedures were (1) designed to ensure that material information relating
to the Company, including its consolidated subsidiaries, is made known to its
President and Chief Executive Officer and its Vice President, Finance and Chief
Financial Officer by others within these entities, particularly during the
period in which this report was being prepared and (2) effective, in that they
provide reasonable assurance that information required to be disclosed by the
Company in the reports that it files or submit under the Exchange Act is
recorded, processed, summarized and reported within the time periods specified
in the SECs rules and forms. No change to the Companys internal control over financial reporting (as
defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) occurred
during the quarter ended March 31, 2004 that has materially affected, or is
reasonably likely to materially affect, the Companys internal control over
financial reporting. 36




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PART II Other Information 
 ITEM 1. LEGAL PROCEEDINGS The description of the legal proceedings set forth under note 8 of the
Companys condensed consolidated financial statements in this Quarterly Report
on Form 10-Q are incorporated herein by reference. 
 ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K (a) The Exhibits listed in the Exhibit index
immediately preceding such Exhibits are filed as part of this Quarterly Report
on Form 10-Q, and such Exhibit Index is incorporated herein by reference. (b) Reports on Form 8-K  1.
    
    Current Report on Form 8-K, furnished on January 13, 2004, announcing
the Companys decision to end efforts to seek U.S. approval of Replagal
and that the Company expected fourth quarter 2003 Replagal sales to
approximate third quarter Replagal sales.2.
    
    Current Report on Form 8-K, furnished on March 11, 2004, announcing
the Companys financial results for the quarter ended March 31, 2004.3.
    
    Current Report on Form 8-K, filed on March 29, 2004, announcing that
Aventis Pharmaceuticals, Inc. has returned
rights to Dynepo to the Company for all indications in Europe and all
other territories outside the United States. 37




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SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized. TRANSKARYOTIC THERAPIES, INC.Date: May 10, 2004
    
    By:
 
/s/ Michael J. AstrueMichael J. AstruePresident and Chief ExecutiveOfficerDate: May 10, 2004
    
    By:
 
/s/ Gregory D. PerryGregory D. PerryVice President, Finance, and ChiefFinancial Officer (PrincipalFinancial and Accounting Officer)
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EXHIBIT INDEX Exhibit No.
    
    Description10.42*#
    
    Amended and Restated License Agreement, dated March 26, 2004,
between Aventis Pharmaceuticals, Inc. and the Registrant31.1*
    
    Certification by the Registrants President and Chief
Executive Officer pursuant to 18 U.S.C. Section 1350, as
adopted pursuant to Section 302 of the Sarbanes-Oxley Act of
2002.31.2*
    
    Certification by the Registrants Vice President, Finance and Chief Financial Officer
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.32.1*
    
    Certification by the Registrants President and 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 Registrants Vice President, Finance and Chief Financial Officer
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to
Section 906 of the Sarbanes-Oxley Act of 2002.
 *
    
    Filed herewith.#
    
    Confidential treatment requested as to certain portions pursuant to Rule
24-b-2 promulgated under the Securities Exchange Act of 1934, as amended.
 39