___________________________________________________________________________

                         SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, D.C.  20549
                            ___________________________
                                          
                                          
                                     FORM 10-Q
                                          

[x] Quarterly report pursuant to Section 13 or 15(d) of the Securities and
    Exchange Act of 1934

    For the quarterly period ended September 30, 1998

                                         OR

[ ] Transition report pursuant to Section 13 or 15(d) of the Securities and
    Exchange Act of 1934

    For the transition period from      to  


                          Commission File Number  000-19319 
                                          
                        Vertex Pharmaceuticals Incorporated
               (Exact name of registrant as specified in its charter)
                                          

          Massachusetts                                        04-3039129
- -------------------------------                             -------------------
(State or other jurisdiction of                              (I.R.S. Employer
incorporation or organization)                               Identification No.)


              130 Waverly Street, Cambridge, Massachusetts  02139-4242
            ------------------------------------------------------------
            (Address of principal executive offices, including zip code)
                                          
                                   (617) 577-6000
                             ----------------------------
                (Registrant's telephone number, including area code)
                                          

     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
                                   ---   ---


     Indicate the number of shares outstanding of each of the issuer's classes
of common stock, as of the latest practicable date.

Common Stock, par value $.01 per share                  25,341,169  
- ---------------------------------------            ---------------------
                Class                          Outstanding at November 10, 1998


           
                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                                       INDEX





                                                                         Page
                                                                       --------
                                                                    
Part I. -  Financial Information
  Item 1. Condensed Consolidated Financial Statements
     
     Report of Independent Accountants                                      3

     Condensed Consolidated Balance Sheets -
          September 30, 1998 and December 31, 1997                          4

     Condensed Consolidated Statements of Operations -
          Three Months Ended September 30, 1998 and 1997                    5

     Condensed Consolidated Statements of Operations -
          Nine Months Ended September 30, 1998 and 1997                     6

     Condensed Consolidated Statements of Cash Flows -
          Nine Months Ended September 30, 1998 and 1997                     7

     Notes to Condensed Financial Statements                                8

  Item 2. Management's Discussion and Analysis of Financial
          Condition and Results of Operations                               10


Part II. -  Other Information                                               15

Signatures                                                                  16
 



                                     2



                         Report of Independent Accountants
                                          
To the Board of Directors and Stockholders of Vertex Pharmaceuticals
Incorporated:

We have reviewed the condensed consolidated balance sheet of Vertex 
Pharmaceuticals Incorporated as of September 30, 1998, and the related 
condensed consolidated statements of operations and cash flows for the three 
month and nine month periods ended September 30, 1998 and 1997. These 
financial statements are the responsibility of the company's management.  

We conducted our review in accordance with standards established by the 
American Institute of Certified Public Accountants. A review of interim 
financial information consists principally of applying analytical procedures 
to financial data and making inquiries of persons responsible for financial 
and accounting matters. It is substantially less in scope than an audit 
conducted in accordance with generally accepted auditing standards, the 
objective of which is the expression of an opinion regarding the financial 
statements taken as a whole. Accordingly, we do not express such an opinion.  

Based on our review, we are not aware of any material modifications that 
should be made to the condensed consolidated financial statements referred to 
above for them to be in conformity with generally accepted accounting 
principles.

We have previously audited, in accordance with generally accepted auditing 
standards, the consolidated balance sheet as of December 31, 1997, and the 
related consolidated statements of operations, stockholders' equity, and cash 
flows for the year then ended (not presented herein); and in our report dated 
February 23, 1998, we expressed an unqualified opinion on those consolidated 
financial statements. In our opinion, the information set forth in the 
accompanying condensed consolidated balance sheet as of December 31, 1997, is 
fairly stated, in all material respects, in relation to the consolidated 
balance sheet from which it has been derived.

PricewaterhouseCoopers LLP

Boston, Massachusetts
October 21, 1998  


                                     3



                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                       CONDENSED CONSOLIDATED BALANCE SHEETS
                                          
                                   (In thousands)
                                    (Unaudited)


 
                                                 September 30,    December 31,
                                                      1998           1997
                                                 --------------   --------------
                                                            

                             ASSETS

Current assets:
   Cash and cash equivalents                         $   49,652    $  71,454
   Short-term investments                               209,261      208,217
   Prepaid expenses and other current assets              1,972        1,952
                                                    -----------    ---------
          Total current assets                          260,885      281,623

Restricted cash                                           2,316        2,316 
Property and equipment, net                              13,709       11,095
Other assets                                                961          570
                                                    -----------    ---------
          Total assets                                $ 277,871    $ 295,604
                                                    -----------    ---------
                                                    -----------    ---------


          LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
   Obligations under capital lease and debt           $   2,840    $   2,510
   Accounts payable and accrued expenses                  8,320       10,632
   Deferred revenue                                         --           556
                                                    -----------    ---------
        Total current liabilities                        11,160       13,698
                                                    -----------    ---------

Obligations under capital leases and debt,
   excluding current portion                              7,629        5,905
                                                    -----------    ---------
        Total liabilities                                18,789       19,603
                                                    -----------    ---------
Stockholders' equity:
   Common stock                                             253          252
   Additional paid-in capital                           394,373      392,372
   Accumulated other comprehensive income                 1,720          152
   Accumulated deficit                                 (137,264)    (116,775)
                                                    -----------    ---------

      Total stockholders' equity                        259,082      276,001
                                                    -----------    ---------
      Total liabilities and stockholders' equity     $  277,871    $ 295,604
                                                    -----------    ---------
                                                    -----------    ---------




                  The accompanying notes are an integral part of 
                 these condensed consolidated financial statements. 


                                     4



                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                  CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                    (Unaudited)
                       (In thousands, except per share data)





                                                     Three Months Ended September 30,
                                                     --------------------------------
                                                            1998          1997
                                                          --------      -------
                                                                  
Revenues:
     Collaborative and other research and
       development                                         $  14,633    $  9,739
     Investment income                                         3,784       3,808
                                                           ---------    --------
          Total revenues                                      18,417      13,547
                                                           ---------    --------

Costs and expenses:
     Research and development                                 15,741      16,449
     General and administrative                                4,772       2,813
     Interest                                                    177         141
                                                           ---------    --------
          Total costs and expenses                            20,690      19,403
                                                           ---------    --------
Net loss                                                    $ (2,273)   $ (5,856)
                                                           ---------    --------
                                                           ---------    --------
Basic and diluted net loss per common share                 $  (0.09)   $  (0.23)
                                                           ---------    --------
                                                           ---------    --------

Basic and diluted weighted average number of 
     common shares outstanding                                25,308      25,119
                                                           ---------    --------
                                                           ---------    --------







                  The accompanying notes are an integral part of 
                 these condensed consolidated financial statements.


                                     5


                                          
                                           
                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                  CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                    (Unaudited)
                      (In thousands, except per share amounts)





                                                          Nine Months Ended September 30,
                                                          --------------------------------
                                                                  1998         1997
                                                                ---------    --------
                                                                       

Revenues:
     Collaborative and other research and development          $  21,053    $  22,719
     Investment income                                            11,685        9,901
                                                               ---------    ---------
          Total revenues                                          32,738       32,620
                                                               ---------    ---------

Costs and expenses:
     Research and development                                     40,554       37,561
     General and administrative                                   12,189        7,654
     Interest                                                        484          438
                                                               ---------    ---------
          Total costs and expenses                                53,227       45,653
                                                               ---------    ---------
Net loss                                                        $(20,489)   $ (13,033)
                                                               ---------    ---------
                                                               ---------    ---------
Basic and diluted net loss per common share                    $   (0.81)   $   (0.54)
                                                               ---------    ---------
                                                               ---------    ---------
Basic and diluted weighted average number of 
     common shares outstanding                                    25,282       23,950
                                                               ---------    ---------
                                                               ---------    ---------










                  The accompanying notes are an integral part of 
                 these condensed consolidated financial statements. 


                                     6



                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                  CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                    (Unaudited)
                                   (In thousands)





                                                                 Nine months ended September 30,
                                                                 -------------------------------
                                                                     1998             1997
                                                                   ---------        ---------
                                                                              
Cash flows from operating activities:
     Net loss                                                      $ (20,489)       $ (13,033)
     Adjustment to reconcile net loss to
          net cash used by operating activities:
            Depreciation and amortization                              3,116            2,565
     Changes in assets and liabilities:
          Prepaid expenses and other 
               current assets                                            (20)            (392)
          Accounts payable and accrued 
               expenses                                               (2,312)           4,379
          Deferred revenue                                              (556)             556
                                                                   ---------        ---------
               Net  cash provided (used) by 
                    operating activities                             (20,261)          (5,925)
                                                                   ---------        ---------
 
Cash flows from investing activities:
     Short-term investments                                              514          (10,468)
     Expenditures for property and equipment                          (5,730)          (4,084)
     Other assets                                                       (391)            (393)
                                                                   ---------        ---------
          Net cash provided (used) by 
               investing activities                                   (5,607)         (14,945)
                                                                   ---------        ---------

Cash flows from financing activities:
     Proceeds from public offering of common stock                      --            148,810
     Proceeds from private placement of common stock                    --             10,000
     Other issuances of common stock                                   2,002            4,776
     Proceeds from equipment sale/leaseback                            4,084            1,855
     Repayment of capital lease obligations                           (2,030)          (2,217)
                                                                   ---------        ---------
          Net cash provided (used) by
               financing activities                                    4,056          163,224
                                                                   ---------        ---------
    
Effect of exchange rate changes on cash                                   10              (14)
                                                                   ---------        ---------
Increase (decrease) in cash and cash equivalents                     (21,802)         142,340 
Cash and cash equivalents at beginning of period                      71,454           34,851
                                                                   ---------        ---------
Cash and cash equivalents at end of period                          $ 49,652        $ 177,191
                                                                   ---------        ---------
                                                                   ---------        ---------



                  The accompanying notes are an integral part of 
                 these condensed consolidated financial statements. 
                                          


                                     7




                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                      NOTES TO CONDENSED FINANCIAL STATEMENTS


1.   Basis of Presentation

     The accompanying condensed consolidated financial statements are 
unaudited and have been prepared by the Company in accordance with generally 
accepted accounting principles. 

     Certain information and footnote disclosures normally included in the 
Company's annual financial statements have been condensed or omitted.  The 
interim financial statements, in the opinion of management, reflect all 
adjustments (including normal recurring accruals) necessary for a fair 
statement of the results for the interim periods ended September 30, 1998 and 
1997.

     The results of operations for the interim periods are not necessarily 
indicative of the results of operations to be expected for the fiscal year, 
although the Company expects to incur a substantial loss for the year ended 
December 31, 1998.  These interim financial statements should be read in 
conjunction with the audited financial statements for the year ended December 
31, 1997, which are contained in the Company's 1997 Annual Report to its 
shareholders and in its Form 10-K filed with the Securities and Exchange 
Commission.

2.   Cash and Cash Equivalents

     For purposes of the statement of cash flows, the Company considers all 
highly liquid investments with maturities of three months or less at the date 
of purchase to be cash equivalents.  Changes in cash and cash equivalents may 
be affected by shifts in investment portfolio maturities as well as by actual 
net cash receipts or disbursements.    

3.   Basic and Diluted Loss per Common Share

     Basic earnings per share is based upon the weighted average number of 
common shares outstanding during the period.  Diluted earnings per share is 
based upon the weighted average number of common shares outstanding during 
the period plus additional weighted average common equivalent shares 
outstanding during the period when the effect is not anti-dilutive.  Common 
equivalent shares result from the assumed exercise of outstanding stock 
options, the proceeds of which are then assumed to have been used to 
repurchase outstanding stock using the treasury stock method.  Common 
equivalent shares have not been included in the per share calculations as the 
effect would be anti-dilutive. Potential common equivalent shares consist of 
5,311,300 stock options outstanding with a weighted average exercise price of 
$22.15 as of September 30, 1998. 


                                     8



                        VERTEX PHARMACEUTICALS INCORPORATED
                                          
                      NOTES TO CONDENSED FINANCIAL STATEMENTS
                                          
4.   Comprehensive Income

          The Company has adopted SFAS No. 130, "Reporting Comprehensive 
Income,"  which requires that all components of comprehensive income and 
total comprehensive income be reported and that changes be shown in a 
financial statement displayed with the same prominence as other financial 
statements.  The Company has elected to disclose this information in its 
statement of stockholders' equity.  For the nine months ended September 30, 
1998 and 1997 total comprehensive loss was as follows (in thousands):         
           


                                                     September 30, 1998      September 30, 1997
                                                    -------------------      ------------------
                                                                       
Net loss                                                $  (20,489)             $  (13,033)

Other comprehensive income (loss):
Unrealized holding gains (losses) on investments             1,559                     116
Foreign currency translation adjustment                         10                     (14)
                                                         ---------               ---------
Total other comprehensive income (loss)                      1,569                     102
                                                         ---------               ---------
Total comprehensive loss                                $  (18,920)             $  (12,931)
                                                         ---------               ---------
                                                         ---------               ---------



5.   Subsequent Event

     In October 1998, the Company earned a $3,000,000 milestone payment from 
Glaxo Wellcome on the submission of a New Drug Application (NDA) for the new 
HIV protease inhibitor Agenerase-TM- (amprenavir).

6.   Recent Collaborative Agreements

     In August 1998, the Company and Schering AG, Germany entered into an 
agreement to collaborate on the research, development and commercialization 
of novel, orally active neurophilin compounds to promote nerve regeneration 
for the treatment of a number of neurological diseases.  Under the terms of 
the agreement, Schering AG will pay the Company up to $88,000,000 composed of 
a $6,000,000 upfront license payment paid in September 1998, $22,000,000 of 
product research funding over five years and $60,000,000 of development and 
commercialization milestone payments.  Under terms of the agreement, Vertex 
and Schering AG will have an equal role in management of neurophilin research 
and product development.  In North America, Vertex will have manufacturing 
rights, and Vertex and Schering AG will share equally in the marketing 
expenses and profits from commercialized compounds. In addition to having 
manufacturing rights in North America, the Company retains the option to 
manufacture bulk drug substance for sales and marketing in territories 
outside Europe, the Middle East and Africa. Schering AG will have the right 
to manufacture and market any commercialized compounds in Europe, the Middle 
East and Africa, and pay Vertex a royalty on product sales.  Schering AG has 
the right to terminate the research agreement without cause upon three 
months' notice after December 1998, but will be obligated to make the 
payments for the period January to December 1999.  After December 2000, 
Schering AG has the right to terminate without cause upon a six months' 
written notice. 


                                     9



7.     Recently Issued Accounting Standards

     In July 1997, the Financial Accounting Standards Board (FASB) issued 
SFAS No. 131, "Disclosures about Segments of an Enterprise and Related 
Information," which is effective for fiscal years beginning after December 
15, 1997.  The interim reporting disclosures are not required in the first 
year of adoption. SFAS 131 specifies revised guidelines for determining an 
entity's operating segments and the type and level of financial information 
to be disclosed.  SFAS 131 changes current practice under SFAS No. 14 by 
establishing a new framework on which to base segment reporting.  The 
"management" approach expands the required disclosures for each segment. The 
Company will adopt SFAS 131 in the fourth quarter ending December 31, 1998 
and has not yet determined the impact of such adoption on its segment 
reporting.

     In June 1998, the FASB issued SFAS No. 133, "Accounting for Derivative 
Instruments and Hedging Activities".  SFAS 133 is effective for all fiscal 
quarters of all fiscal years beginning after June 15, 1999.  SFAS 133 
requires that all derivative instruments be recorded on the balance sheet at 
their fair value.  Changes in the fair value of derivatives are recorded each 
period in current earnings or other comprehensive income, depending on 
whether a derivative is designated as part of a hedge transaction and if it 
is, the type of hedge transaction.  The Company is currently assessing the 
impact of this SFAS 133 does not believe that it will have a material impact 
on the financial statements. 

8.      Legal Proceedings
     
     Chiron Corporation ("Chiron") filed suit on July 30, 1998 against the 
Company and Eli Lilly and Company in the United States District Court for the 
Northern District of California, alleging infringement by the defendants of 
various U.S. patents issued to Chiron.  The infringement action relates to 
research activities by the defendants in the hepatitis C viral protease field 
and the alleged use of inventions claimed by Chiron in connection with that 
research and development.  Chiron has requested damages in an unspecified 
amount, as well as an order permanently enjoining the defendants from 
unlicensed use of Chiron inventions.  The Company intends to vigorously 
contest the action.

                 MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                        CONDITION AND RESULTS OF OPERATIONS

This discussion contains forward-looking statements which are subject to 
certain risks and uncertainties that can cause actual results to differ 
materially from those described.  Factors that may cause such differences 
include but are not limited to those described in the section of the 
Company's annual report on Form 10-K entitled "Risk Factors."  Readers are 
cautioned not to place undue reliance on these forward-looking statements 
which speak only as of the date hereof.  The Company undertakes no obligation 
to publicly update or revise these forward-looking statements to reflect 
events or circumstances after the date hereof.

     Since its inception in 1989, the Company has been engaged in the 
discovery, development and commercialization of novel, small molecule 
pharmaceuticals for the treatment of major diseases for which there are 
currently limited or no effective treatments.  The Company is a leader in the 
use of structure-based drug design, an approach to drug discovery that 
integrates advanced biology, biophysics and chemistry.  The company is 
conducting research and development programs to develop pharmaceuticals for 
the treatment of viral diseases, multidrug resistance in cancer, autoimmune 
and inflammatory diseases and neurodegenerative disorders.  


                                     10


 
     To date, the Company has not received any revenues from the sale of 
pharmaceutical products.  The Company's lead product candidate, 
Agenerase-TM-(amprenavir) for the treatment of HIV infection, is presently 
undergoing Phase III clinical trials.  A New Drug Application ("NDA") was 
submitted to the U.S. Food and Drug Administration in October 1998, and 
equivalent applications were subsequently submitted to Canadian and European 
regulatory agencies.  If the clinical trials are concluded successfully and 
if the NDA is approved by the FDA, and product sales commence, the Company 
will receive a royalty on sales of Agenerase-TM- by its partner Glaxo 
Wellcome plc ("Glaxo Wellcome").  However, there can be no assurance that 
Phase III clinical trials will be successfully completed, or that marketing 
approval will be granted by the FDA.  The Company has incurred operating 
losses since its inception and expects to incur a loss in 1998.  The Company 
believes that operating losses may continue for the next several years even 
if significant royalties are realized on Agenerase-TM- sales because the 
Company is planning to make significant investments in research and 
development for its other potential products.  The Company expects that 
losses will fluctuate from quarter to quarter and that such fluctuations may 
be substantial.

Results of Operations

Three Months Ended September 30, 1998 Compared with Three Months Ended September
30, 1997. 

     The Company's total revenues increased to $18,417,000 in the third 
quarter of 1998 from $13,547,000 in the third quarter of 1997. In the third 
quarter of 1998, revenues consisted of $14,407,000 under the Company's 
collaborative agreements, $3,784,000 in investment income and $226,000 in 
government grants and other revenue.  In the third quarter of 1997, the 
Company received $9,380,000 in revenue from its collaborative agreements, 
$3,808,000 in investment income and $359,000 from government grants and other 
revenue. Revenues for the third quarter in 1998 included $9,000,000 of 
payments from Schering AG, under a new collaboration (the "Schering 
Agreement") signed in August 1998 to research, develop and commercialize 
novel, orally active neurophilin compounds that promote nerve growth and 
repair.  The payment included $3,000,000 in research funding for the period 
from January 1, 1998 to September 30, 1998, and a $6,000,000 license fee.  
Also in the third quarter 1998, Vertex received a $2,000,000 milestone 
payment from Kissei Pharmaceutical Co., Ltd. ("Kissei") relating to the 
selection of Vertex's compound VX-745 as a lead drug development candidate 
targeting the p38 MAP kinase enzyme.  Revenues for the third quarter of 1998 
increased even though 1997 third quarter revenues included a $4,000,000 
up-front payment and $750,000 in research funding received from Kissei under 
the collaborative agreement  for the Company's p38 MAP kinase program, signed 
in September 1997, and the reimbursement by Hoechst Marion Roussel ("HMR") of 
certain costs associated with the Company's ICE program.

     The Company's total costs and expenses increased to $20,690,000 in the 
third quarter of 1998 from $19,403,000 in the third quarter of 1997. Research 
and development expenses decreased to $15,741,000 in the third quarter of 
1998 from $16,449,000 in the third quarter of 1997. In the third quarter of 
1998, the Company experienced lower clinical and preclinical development 
expenses for its MDR program for cancer, the ICE program for inflammatory 
diseases and the IMPDH program for autoimmune diseases.  These decreases were 
offset in part by headcount growth of the scientific organization and by 
commencement of research activities at the Company's new U.K. research 
facility.  General and administrative expenses increased to $4,772,000 in the 
third quarter of 1998 from $2,813,000 in the third quarter of 1997. The 
increase in general and administrative expenses principally reflects the 
impact of personnel additions and an increase in marketing activities in 
preparation for the anticipated launch of Agenerase-TM-.  Interest expense 
increased to $177,000 in the third quarter of 1998 from $141,000 in the third 
quarter of 1997 due to higher levels of equipment lease financing during the 
year.  The Company expects that research and development as well as general 
and administrative expenses will continue to increase as the Company starts 
new research projects, advances current clinical and preclinical candidates, 
and expands its marketing and business development activities.

     The Company recorded a net loss of $2,273,000 or $0.09 per share in the 
third quarter of 1998 compared to a net loss of $5,856,000 or $0.23 per share 
in the third quarter of 1997.


                                     11



Nine Months Ended September 30, 1998 Compared with Nine Months Ended September
30, 1997.  

     The Company's total revenues were $32,738,000 for the nine months ended 
September 30, 1998 as compared to $32,620,000 for the nine months ended 
September 30, 1997.  In 1998, the Company's revenues consisted of $20,368,000 
in collaborative revenues, $11,685,000 in investment income, and $685,000 in 
government grants and other income.  In 1997, the Company's revenues 
consisted of $21,439,000 earned under the Company's collaborative agreements, 
$9,901,000 in investment income and $1,280,000 in government grants and other 
income. While the 1998 first three quarters revenue included $9,000,000 of 
payments from Schering AG, there was a moderate decline relative to the 1997 
period due to the Company's receipt in 1997 of $4,000,000 in development 
reimbursements from Kissei for a clinical trial of Agenerase-TM-, $3,000,000 
of upfront payments from Lilly for the Company's Hepatitis C program and 
$4,000,000 from Kissei for the p38 MAP Kinase program.  

     The Company's total costs increased to $53,227,000 for the nine months 
ended September 30, 1998 from $45,653,000 for the nine months ended September 
30, 1997. Research and development expenses increased to $40,554,000 in the 
first three quarters of 1998 from $37,561,000 in the first three quarters of 
1997, primarily due to the expansion of the Company's research and 
development activities. General and administrative expenses increased during 
the first three quarters of 1998 to $12,189,000 from $7,654,000 in the first 
three quarters of 1997 due primarily to increases in personnel and 
professional expenses, particularly in preparation for the expected market 
launch of Agenerase-TM- and corporate advertising activities.  Interest 
expense was $484,000 in the first three quarters of 1998, an increase from 
$438,000 in the first three quarters of 1997 as a result of higher levels of 
equipment financing during the period.

     For the reasons stated above, the Company incurred a net loss of 
$20,489,000 or $0.81 per share in the nine months ended September 30, 1998 
compared to a net loss of $13,033,000 or $0.54 per share in the nine months 
ended September 30, 1997.

Liquidity and Capital Resources

     The Company's operations have been funded principally through strategic 
collaborative agreements, public offerings and private placements of the 
Company's equity securities, equipment lease financing, government grants and 
investment income.  The Company expects to incur increased research and 
development and related supporting expenses and, consequently, may continue 
to experience losses on a quarterly and annual basis as it continues to 
develop existing and future compounds and to conduct clinical trials of 
potential drugs. The Company also expects to incur substantial administrative 
and commercialization expenditures in the future and additional expenses 
related to the filing, prosecution, defense and enforcement of patent and 
other intellectual property rights.

     The Company expects to finance these substantial cash needs with its 
existing cash and investments of approximately $258,913,000 at September 30, 
1998, together with investment income earned thereon, future payments under 
its existing collaborative agreements, and facilities and equipment 
financing.  In addition, an NDA for Agenerase-TM- was submitted in October 
which, if approved, will lead to royalty income. To the extent that funds 
from these sources are not sufficient to fund the Company's activities, it 
will be necessary to raise additional funds through public offerings or 
private placements of securities or new research collaborations for new or 
existing projects, or other methods of financing.  There can be no assurance 
that such financing will be available on acceptable terms, if at all.  The 
Company believes that its existing cash and investments should be sufficient 
to meet its anticipated requirements for at least the next two years.

     The Company's aggregate cash and investments decreased by $20,758,000 
during the nine months ended September 30, 1998 to $258,913,000.  Cash used 
by operations, principally to fund research and development activities, was 
$20,261,000 during the same period.  The Company also expended $5,730,000 
during this period to acquire property and equipment, principally for 
research equipment and 


                                     12



facilities.  During the first three quarters of 1998, the Company entered 
into equipment financing arrangements in the aggregate amount of $4,084,000 
and repaid $2,030,000 of its lease obligations.

     In addition to the expansion of the research and development activities 
in the U.S., the Company started the expansion of its U.K. operations to 
include a research site during the third quarter in 1998. The Company expects 
that, in general, research and development as well as general and 
administrative expenses will continue to increase as the Company starts new 
research projects, advances current clinical and preclinical candidates, and 
expands its marketing and business development activities.

     Under the terms of the Schering Agreement, Schering AG will pay the 
Company up to $88,000,000 composed of a $6,000,000 upfront license payment 
paid in September 1998, $22,000,000 of product research funding over five 
years and $60,000,000 of development and commercialization milestone 
payments. 

     The Company adopted requirements relating to comprehensive income in 
accordance with the Statement of Financial Accounting Standards No. 130 
("SFAS 130"), "Reporting Comprehensive Income".  This Statement requires that 
total comprehensive income be reported and that changes be shown in a 
financial statement displayed with the same prominence as other financial 
statements.

     In July 1997, the Financial Accounting Standards Board (FASB) issued 
SFAS No. 131, "Disclosures about Segments of an Enterprise and Related 
Information", which is effective for fiscal years beginning after December 
15, 1997.  The interim reporting disclosures are not required in the first 
year of adoption. SFAS 131 specifies revised guidelines for determining an 
entity's operating segments and the type and level of financial information 
to be disclosed.  SFAS 131 changes current practice under SFAS No. 14 by 
establishing a new framework on which to base segment reporting.  The 
"management" approach expands the required disclosures for each segment. The 
Company will adopt SFAS 131 in the fourth quarter ended December 31, 1998 and 
has not yet determined the impact of such adoption on its segment reporting.

     In June 1998, the FASB issued SFAS No. 133, "Accounting for Derivative 
Instruments and Hedging Activities".  SFAS 133 is effective for all fiscal 
quarters of all fiscal years beginning after June 15, 1999.  SFAS 133 
requires that all derivative instruments be recorded on the balance sheet at 
their fair value.  Changes in the fair value of derivatives are recorded each 
period in current earnings or other comprehensive income, depending on 
whether a derivative is designated as part of a hedge transaction and if it 
is, the type of hedge transaction.  The Company is currently assessing the 
impact of this FASB and does not believe that it will have a material impact 
on the financial statements.    
     
Year 2000

The Company is currently assessing the potential impact of the Year 2000 on 
the processing of date-sensitive information by the Company's computerized 
information systems and products purchased by the Company.  The Company's 
review includes its own computer systems and software ("IT Systems"), 
embedded systems in its non-computer equipment ("Non-IT Systems"), and 
relationships with certain third parties.

The Company has completed its evaluation of its business critical IT Systems 
and has determined the actions necessary in order to ensure that such IT 
Systems will be able to function without disruption with respect to the 
application of dating systems in the Year 2000.  The Company has begun to 
upgrade, replace  and test certain of its IT Systems based on the results of 
that evaluation. Evaluation of Non-IT Systems for Year 2000 compliance is 
under way but has not been completed.

In addition to risks associated with the Company's own computer systems and 
equipment, the Company has relationships with, and is to varying degrees 
dependent upon, a number of third parties that provide goods, services and 
information to the Company. These include contract manufacturers, suppliers, 


                                     13




licensees and licensors, vendors, research partners and financial 
institutions, whose systems and equipment are outside the control of the 
Company.  If certain of these third parties experience failures in their 
computer systems or equipment due to Year 2000 non-compliance, it could 
affect the Company's ability to engage in normal business activities. The 
Company intends to contact its significant vendors and partners to ascertain 
their Year 2000 compliance and to determine the extent to which the Company 
is vulnerable to their non-compliance, if any.
     
The Company expects to complete its internal evaluation and remediation 
efforts and its assessment of third party compliance by mid-1999.  However, 
there can be no assurance that these evaluations and any required remedial 
actions will be able to be completed on a timely basis. The Company believes 
that its internal IT Systems and Non-IT Systems are either already Year 2000 
compliant or will be so prior to the Year 2000 without incurring material 
costs. There can be no assurance, however, that the Company will not 
experience unexpected costs in achieving Year 2000 compliance for its 
internal systems, which could result in a material adverse effect on the 
Company's future results of operations. The Company believes that it will be 
able to locate alternate sources for any critical goods or services provided 
by non-compliant third parties, if any. However, the Company may not be able 
to timely develop or implement contingency plans to address those business 
critical systems and third party relationships which may not be Year 2000 
compliant.




                                     14


 

                                      PART II.
                                          
                                 OTHER INFORMATION
                                          


Item 1.   Legal Proceedings:

     Chiron Corporation ("Chiron") filed suit on July 30, 1998 against the
Company and Eli Lilly and Company in the United States District Court for the
Northern District of California, alleging infringement by the defendants of
various U.S. patents issued to Chiron.  The infringement action relates to
research activities by the defendants in the hepatitis C viral protease field
and the alleged use of inventions claimed by Chiron in connection with that
research and development.  Chiron has requested damages in an unspecified
amount, as well as an order permanently enjoining the defendants from unlicensed
use of Chiron inventions.  The Company intends to vigorously contest the action.

Item 2.   Changes in Securities:

          None

Item 3.   Defaults Upon Senior Securities:

          None

Item 4.   Submission of Matters to a Vote of Security Holders:

          None

Item 5.   Other Information:

          None

Item 6.   Exhibits:

          10.1   Research Agreement dated August 24, 1998 between the
                 Company and Schering AG. (Filed herewith with certain 
                 confidential information omitted. The omitted portions have 
                 been filed separately with the Securities and Exchange 
                 Commission pursuant to a request for confidential treatment.)

           27    Financial Data Schedule. (Exhibit 27 is submitted as an exhibit
                 only in the electronic format of this Quarterly Report on 
                 Form 10-Q submitted to the Securities and Exchange Commission.)

           99    Letter of Independent Accountants 

          Reports on Form 8-K:

           None



                                     15




                                     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.

                        VERTEX PHARMACEUTICALS INCORPORATED




Date:  November 13, 1998               /s/ Thomas G. Auchincloss
                                       -------------------------
                                       Thomas G. Auchincloss, Jr.
                                       Vice President of Finance and Treasurer
                                       (Principal Financial Officer) 



Date:  November 13, 1998               /s/ Hans D. van Houte
                                       --------------------------------------
                                       Hans D. van Houte
                                       Controller
                                       (Principal Accounting Officer)



                                     16