- -------------------------------------------------------------------------------
- -------------------------------------------------------------------------------

                      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, 1997
                                      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  0-19319   
                                               ---------
                                           
                      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                 25,196,342        
- --------------------------------------      -------------------------------
               Class                        Outstanding at November 6, 1997
         

                                       1
 

 
                         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, 1997 and December 31, 1996                4

              Condensed Consolidated Statements of Operations -
                    Three Months Ended September 30, 1997 and 1996          5

              Condensed Consolidated Statements of Operations -
                    Nine Months Ended September 30, 1997 and 1996           6

              Condensed Consolidated Statements of Cash Flows -
                    Nine Months Ended September 30, 1997 and 1996           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                                              14
 
Signatures                                                                 15

                                       2



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

We have reviewed the accompanying condensed consolidated balance sheet of 
Vertex Pharmaceuticals Incorporated as of September 30, 1997, and the related 
condensed consolidated statements of operations and cash flows for the three 
month and the nine month periods ended September 30, 1997 and 1996. 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, 1996, and the 
related consolidated statements of  operations, retained earnings, and cash 
flows for the year then ended (not presented herein); and in our report dated 
February 18, 1997, 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, 1996, is 
fairly stated, in all material respects, in relation to the consolidated 
balance sheet from which it has been derived.


                                       /s/ COOPERS & LYBRAND L.L.P.



 Boston, Massachusetts
 October 21, 1997

                                       3


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



                                                                     September 30,            December 31,
                                                                         1997                     1996
                                                                     -------------            ------------
                                                                                        

                                               ASSETS
                                           
Current assets:
   Cash and cash equivalents                                           $ 177,191                $  34,851
   Short-term investments                                                106,092                   95,508
   Prepaid expenses and other current assets                               2,183                    1,791
                                                                     -------------            ------------

       Total current assets                                              285,466                  132,150

Restricted cash                                                            2,316                    2,316
Property and equipment, net                                               10,182                    8,663
Other assets                                                                 763                      370
                                                                     -------------            ------------

       Total assets                                                    $ 298,727                $ 143,499
                                                                     -------------            ------------
                                                                     -------------            ------------


                               LIABILITIES AND STOCKHOLDERS' EQUITY
                                           
Current liabilities:
   Obligations under capital lease and debt                            $   2,677                $   2,910
   Accounts payable and accrued expenses                                   8,525                    4,146
   Deferred revenue                                                          556                      ---
                                                                     -------------            ------------

       Total current liabilities                                          11,758                    7,056
                                                                     -------------            ------------

Obligations under capital leases and debt, excluding
   current portion                                                         5,488                    5,617
                                                                     -------------            ------------

       Total liabilities                                                  17,246                   12,673
                                                                     -------------            ------------

Stockholders' equity:
   Common stock                                                              251                      211
   Additional paid-in capital                                            391,056                  227,510
   Equity adjustments                                                        151                       49
   Accumulated deficit                                                  (109,977)                 (96,944)
                                                                     -------------            ------------

       Total stockholders' equity                                        281,481                  130,826
                                                                     -------------            ------------

       Total liabilities and stockholders' equity                      $ 298,727                $ 143,499
                                                                     -------------            ------------
                                                                     -------------            ------------


                 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,
                                                           --------------------------------

                                                                 1997             1996
                                                              ----------       ----------
                                                                         

Revenues:
   Collaborative and other research and development            $  9,739         $  2,930
   Interest income                                                3,808            1,190
                                                              ----------       ----------

       Total revenues                                            13,547            4,120
                                                              ----------       ----------


Costs and expenses:
   Research and development                                      16,449            8,525
   General and administrative                                     2,813            1,832
   Interest                                                         141              109
                                                              ----------       ----------

       Total costs and expenses                                  19,403           10,466
                                                              ----------       ----------

Net loss                                                       $ (5,856)        $ (6,346)
                                                              ----------       ----------
                                                              ----------       ----------

Net loss per common share                                      $  (0.23)        $  (0.33)
                                                              ----------       ----------
                                                              ----------       ----------


Weighted average number of common shares
   outstanding                                                   25,119           19,364
                                                              ----------       ----------
                                                              ----------       ----------




                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,
                                                            -------------------------------

                                                                 1997             1996
                                                              ----------       ----------
                                                                         

Revenues:
   Collaborative and other research and development            $ 22,719         $  8,519
   Interest income                                                9,901            3,498
                                                              ----------       ----------

       Total revenues                                            32,620           12,017
                                                              ----------       ----------

Costs and expenses:
   Research and development                                      37,561           27,352
   General and administrative                                     7,654            5,473
   License payment                                                  ---           15,000
   Interest                                                         438              331
                                                              ----------       ----------

       Total costs and expenses                                  45,653           48,156
                                                              ----------       ----------

Net loss                                                       $(13,033)        $(36,139)
                                                              ----------       ----------
                                                              ----------       ----------

Net loss per common share                                      $  (0.54)        $  (2.00)
                                                              ----------       ----------
                                                              ----------       ----------


Weighted average number of common shares
   outstanding                                                   23,950           18,036
                                                              ----------       ----------
                                                              ----------       ----------



                 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,
                                                            -------------------------------

                                                                 1997             1996
                                                              ----------       ----------
                                                                         

Cash flows from operating activities:
   Net loss                                                    $(13,033)        $(36,139)
   Adjustments to reconcile net loss to
      net cash used by operating activities:
      Depreciation and amortization                               2,565            2,534
      Changes in assets and liabilities:
        Prepaid expenses and other
          current assets                                           (392)              18
        Accounts payable and accrued
          expenses                                                4,379           (3,607)
        Deferred revenue                                            556             (197)
                                                              ----------       ----------
          Net cash provided (used) by
            operating activities                                 (5,925)         (37,391)
                                                              ----------       ----------

Cash flows from investing activities:
   Net purchases and sales of short-term investments            (10,468)         (33,767)
   Expenditures for property and equipment                       (4,084)          (1,708)
   Other assets                                                    (393)            (869)
                                                              ----------       ----------
          Net cash provided (used) by
            investing activities                                (14,945)         (36,344)
                                                              ----------       ----------

Cash flows from financing activities:
   Net proceeds from public offerings of common stock           148,810           77,539
   Proceeds from private placement of common stock               10,000            5,000
   Other issuances of common stock                                4,776            2,039
   Proceeds from equipment sale/leaseback and debt                1,855            1,488
   Repayment of capital lease obligations                        (2,217)          (1,598)
                                                              ----------       ----------
          Net cash provided (used) by
            financing activities                                163,224           84,468
                                                              ----------       ----------

Effect of exchange rate changes on cash                             (14)               1
                                                              ----------       ----------

Increase (decrease) in cash and cash equivalents                142,340           10,734

Cash and cash equivalents at beginning of period                 34,851           28,390
                                                              ----------       ----------

Cash and cash equivalents at end of period                     $177,191         $ 39,124
                                                              ----------       ----------
                                                              ----------       ----------



                 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 year end condensed balance sheet data was derived from audited 
financial statements. Certain information and footnote disclosures normally 
included in the Company's annual financial statements prepared in accordance 
with generally accepted accounting principles 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, 1997 and 
1996.

    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, 1997.  These interim financial statements should be read in 
conjunction with the audited financial statements for the year ended December 
31, 1996, which are contained in the Company's 1996 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.  Net Loss per Common Share

    The net loss per common share is computed based upon the weighted average 
number of common shares outstanding.  Common equivalent shares are not 
included in the per-share calculations where the effect would be 
anti-dilutive.

4.  Recently Issued Accounting Standards

    The Financial Accounting Standards Board ("FASB") has issued Statement of 
Financial Accounting Standards No. 128 ("SFAS 128"), "Earnings Per Share"  
which modifies the way in which earnings per share ("EPS") is calculated and 
disclosed.  SFAS 128 requires a dual presentation of basic and diluted EPS 
for all years presented in the income statements.  SFAS 128 is effective for 
financial statements for periods ending after December 15, 1997.  The 
adoption of SFAS 128 is not expected to have a material impact on the 
Company's EPS calculation.

    The FASB has recently issued 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. SFAS 130 is effective for fiscal years beginning after 
December 15, 1997. Reclassification of financial statements for earlier 
periods is required for comparative purposes.  The Company does not  believe 
that this will have a material impact on results of operations.

                                       8



 
                         VERTEX PHARMACEUTICALS INCORPORATED
                                           
                       NOTES TO CONDENSED FINANCIAL STATEMENTS
                                           
                                           
5.  Recent Collaborative Agreements

    In September 1997, the Company and Kissei Pharmaceutical Co. Ltd. 
("Kissei") entered into a collaborative agreement to design inhibitors of p38 
MAP Kinase and to develop them as novel, orally active drugs for the 
treatment of inflammatory and neurological diseases.  Under the terms of the 
agreement, Kissei will pay the Company up to $22 million composed of a $4 
million research funding payment paid in September 1997, $11 million of 
product research funding over three years and $7 million of development and 
commercialization milestone payments.  The Company and Kissei will 
collaborate to identify and evaluate compounds that target p38 MAP Kinase.  
Kissei will have the right to develop and commercialize these compounds in 
its licensed territories.  Kissei has exclusive rights to p38 MAP Kinase 
compounds in Japan and certain Southeast Asian countries and semi-exclusive 
rights in China, Taiwan and South Korea.  The Company retains exclusive 
marketing rights in the United States, Canada, Europe, and the rest of the 
world.  In addition, the Company will have the right to supply bulk drug 
material to Kissei for sale in its territory, and will receive royalties and 
drug supply payments on any product sales.  Kissei has the right to terminate 
the agreement without cause upon six months' notice after June 1998.

    In June 1997, the Company and Eli Lilly and Company ("Lilly") entered 
into a collaborative agreement  to design inhibitors of the hepatitis C 
protease enzyme, and to develop them as novel drugs to treat hepatitis C 
infection. Under the terms of the agreement, Lilly will pay the Company up to 
$51 million composed of a $3 million research funding payment paid in June 
1997, $33 million of product research funding over six years and $15 million 
of development and commercialization milestone payments.  The Company and 
Lilly will jointly manage the research, development, manufacturing and 
marketing of drug candidates emerging from the collaboration.  The Company 
will have primary responsibility for drug design, process development and 
pre-commercial drug substance manufacturing, and Lilly will have primary 
responsibility for formulation, preclinical and clinical development and 
global marketing.  The Company has the option to supply 100 percent of 
Lilly's commercial drug substance supply needs. The Company will receive 
royalties on future product sales, if any.  If the Company exercises its 
commercial supply option, the Company will receive drug supply payments in 
addition to royalties on future product sales, if any.  Lilly has the right 
to terminate the agreement without cause upon six months' notice after June 
1999.  In connection with this collaboration, Lilly purchased 263,922 shares 
of the Company's common stock for $10,000,000.

                                           
                                       9



                         VERTEX PHARMACEUTICALS INCORPORATED
                                           
                  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                         CONDITION AND RESULTS OF OPERATIONS
                                           
    The Company is 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 nine significant 
pharmaceutical research and development programs to develop pharmaceuticals 
for the treatment of viral diseases, multidrug resistance in cancer, 
autoimmune diseases, inflammatory diseases and neurodegenerative disorders.  
Four of these programs are in the development phase, and the other four are 
in the research phase.  During the third quarter of 1997, the Company's 
partner, Glaxo Wellcome plc ("Glaxo Wellcome"), advanced Phase III clinical 
development of VX-478 (141W94), the lead compound in the Company's HIV 
program, in the United States, Canada and Europe.  Kissei is also developing 
VX-478 as the Company's partner for the HIV program in the Far East. Through 
a series of Phase II clinical trials underway, the Company and its partner 
for development and marketing of VX-710 in Canada, BioChem Therapeutics Inc. 
("BioChem"), are evaluating VX-710 for the reversal of cancer multidrug 
resistance in solid tumors.  During the quarter, the Company and Alpha 
Therapeutic ("Alpha") terminated their agreement to develop VX-366, an oral 
compound for the treatment of inherited hemoglobin disorders, including 
sickle cell anemia and beta thalassemia.  In addition, the Company signed a 
research, development and commercialization agreement with Kissei to develop 
new drugs targeting p38 MAP Kinase to treat inflammatory and neurological 
diseases.

    To date, the Company has not received any revenues from the sale of 
pharmaceutical products and does not expect to receive such revenues this 
fiscal year, if ever.  The Company has incurred since its inception, and may 
incur over the next several years, significant operating losses as a result 
of expenditures for its research and development programs.  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, 1997 Compared with Three Months Ended 
September 30, 1996.  For the third quarter of 1997, the Company's total 
revenues were $13,547,000 as compared to $4,120,000 during the same period in 
1996.  From quarter to quarter, the Company's revenues fluctuate as a result 
of changes in the timing and amount of partner research support payments, 
partner reimbursements of Vertex drug development costs, and payments for the 
achievement of various research and development milestones.  In the third 
quarter of 1997, the Company received $9,380,000 in revenue from its 
collaborative agreements, $3,808,000 in interest received on invested funds 
and $359,000 from government grants and  other revenue.  In the third quarter 
of 1996, the Company received $2,678,000 in revenue from its collaborative 
agreements, $1,190,000 in interest earned on invested funds and $252,000 from 
government grants and other revenue.  The increase in collaborative revenue 
for the third quarter in 1997 is attributable principally to the $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, the reimbursement by Hoechst Marion Roussel ("HMR") of 
certain costs associated with the Company's ICE program, and research funding 
from Lilly under a research collaboration signed in June 1997.

                                      10




                        VERTEX PHARMACEUTICALS INCORPORATED
                                           
                  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                         CONDITION AND RESULTS OF OPERATIONS
                                           
                                           
    The Company's total costs and expenses increased to $19,403,000 in the 
third quarter of 1997, from $10,466,000 during the same period in 1996. 
Research and development expenses were $16,449,000 in the third quarter of 
1997 as compared to $8,525,000 during the same period in 1996.  This increase 
in expense was principally a result of the continued growth of the Company's 
research and development organization, ongoing clinical trials in the 
multidrug resistance program, and preclinical development expenses for the 
VX-740, the Company's lead compound in the ICE program, and VX-497, the lead 
compound in the IMPDH program.  In addition, during the third quarter of 
1997, the Company purchased a portfolio of ten patent application families 
claiming interleukin 1 beta converting enzyme ("ICE") and its inhibitors from 
Sanofi S.A.  General and administrative expenses increased during the third 
quarter of 1997 to $2,813,000 from $1,832,000 in the third quarter of 1996 
due primarily to increases in administrative personnel, increased legal costs 
associated with patents and other matters, as well as an increase in 
marketing efforts by the Company and the Company's subsidiary Altus Biologics 
Inc. ("Altus").  Interest expense increased to $141,000 in the third quarter 
of 1997 as compared to $109,000 during the same period in 1996 due to higher 
levels of equipment financing.

    The Company incurred a net loss of $5,856,000 or $0.23 per share in the 
third quarter of 1997 as compared to a net loss of $6,346,000 or $0.33 per 
share in the third quarter of 1996.

    Nine Months Ended September 30, 1997 Compared with Nine Months Ended 
September 30, 1996.  The Company's total revenues increased to $32,620,000 
for the nine months ended September 30, 1997 from $12,017,000 for the nine 
months ended September 30, 1996.   In 1997, the Company's revenues consisted 
of $21,439,000 earned under the Company's collaborative agreements, 
$9,901,000 in interest income and $1,280,000 in government grants and other 
income.  In 1996, the Company's revenues consisted of $7,825,000 earned under 
the Company's collaborative agreements, $3,498,000 in interest income and 
$694,000 in government grants and other income.  The increase in revenue 
during 1997 compared to the same period in 1996 was principally due to the 
new collaborative agreements signed in 1997, an increase in development 
reimbursements, and higher investment income.  The Company received 
$4,000,000 from Kissei upon the commencement of the p38 MAP Kinase 
collaboration in September 1997, an upfront payment of $3,000,000 from Lilly 
upon the commencement of the hepatitis C collaboration in June 1997, and 
reimbursements of certain development costs by Kissei and HMR associated with 
the Company's HIV and ICE programs including $4,000,000 from Kissei in the 
first three quarters of 1997. The increase in investment income was due to 
higher levels of cash and investments resulting from public offerings of the 
Company's stock in March 1997 and August 1996.
 
    The Company's total costs decreased to $45,653,000 for the nine months 
ended September 30, 1997 from $48,156,000 for the nine months ended September 
30, 1996. In the second quarter of 1996, the Company paid $15,000,000 to 
obtain a non-exclusive, worldwide license under certain G.D. Searle and 
Company patent applications claiming HIV protease inhibitors.  Research and 
development expenses increased to $37,561,000 in the first nine months of 
1997 from $27,352,000 in the first nine months of 1996, due to additional 
scientific staffing, ongoing Phase II clinical trials for the Company's 
multidrug resistance program, purchase of a patent applications portfolio, as 
well as the commencement of preclinical activities for VX-740, the Company's 
lead compound in the ICE program, and VX-497, the lead compound in the IMPDH 
program.

                                      11



                          VERTEX PHARMACEUTICALS INCORPORATED
                                           
                  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                         CONDITION AND RESULTS OF OPERATIONS
                                           
                                           
    General and administrative expenses increased during the first nine 
months of 1997 to $7,654,000 from $5,473,000 in the first nine months of 1996 
due primarily to increases in administrative personnel, increased legal costs 
associated with patents and other matters, as well as an increase in 
marketing efforts of the Company and Altus.  Interest expense was $438,000 in 
the first nine months of 1997, an increase from $331,000 in the first nine 
months of 1996, as a result of higher levels of equipment financing during 
the period.

    For the reasons stated above, the Company incurred a net loss of 
$13,033,000 or $0.54 per share in the nine months ended September 30, 1997 
compared to a net loss of $36,139,000 or $2.00 per share in the nine months 
ended September 30, 1996.
                                           
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 
interest income.  The Company expects to incur increased research and 
development and related supporting expenses and, consequently, may incur 
continued 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 at September 30, 1997 of approximately $283 
million, together with interest earned thereon, future payments under its 
existing collaborative agreements, and facilities and equipment financing.  
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 other methods of 
financing.  There can be no assurance that such financing will be available 
on acceptable terms, if at all.

    In September 1997, the Company entered into a collaborative agreement for 
up to $22 million with Kissei for the research, development and 
commercialization of compounds in connection with the Company's p38 MAP 
Kinase program.  The Company will supply bulk drug material to Kissei for 
sale in its territory, and will receive royalties and drug supply payments on 
product sales, if any.

    In August 1997, the Company and Alpha terminated their agreement to 
develop VX-366, an oral compound for the treatment of inherited hemoglobin  
disorders, including sickle cell anemia and beta thalassemia. This 
termination does not have a material effect on the liquidity and capital 
resources of the Company.

    In June 1997, the Company and Lilly entered into a collaborative 
agreement to design inhibitors of the hepatitis C protease enzyme, and to 
develop them as novel drugs to treat hepatitis C infection.The Company has 
the option to supply 100 percent of Lilly's commercial drug substance supply 
needs.  The Company will receive royalties on future product sales, if any.  
If the Company exercises its commercial supply option, the Company will 
receive drug supply payments in addition to royalties on future product 
sales, if any. In connection with this collaboration, Lilly purchased 263,922 
shares of the Company's common stock for $10,000,000.                         

                                      12



                         VERTEX PHARMACEUTICALS INCORPORATED
                                           
                  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                         CONDITION AND RESULTS OF OPERATIONS
                                           

    The Company's aggregate cash and investments increased by $152,924,000 
during the nine months ended September 30, 1997 to $283,283,000, principally 
due to a public offering of common stock completed in March 1997, with net 
proceeds of approximately $148,810,000, and an equity investment by Lilly in 
June 1997 of $10,000,000.  Cash used by operations, principally to fund 
research and development activities, was $5,925,000 during the same period.  
The Company also expended $4,084,000 during this period to acquire property 
and equipment, principally for research equipment and facilities.  During the 
first nine months of 1997, the Company entered into equipment lease financing 
in the aggregate amount of $1,855,000 and repaid $2,217,000 of its lease 
obligations.

    The Financial Accounting Standards Board ("FASB") has issued Statement of 
Financial Accounting Standards No. 128 ("SFAS 128"), "Earnings Per Share"  
which modifies the way in which earnings per share ("EPS") is calculated and 
disclosed.  SFAS 128 requires a dual presentation of basic and diluted EPS 
for all years presented in the income statements.  SFAS 128 is effective for 
financial statements for periods ending after December 15, 1997.  The 
adoption of SFAS 128 is not expected to have a material impact on the 
Company's EPS calculation.  The FASB has also issued 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. SFAS 130 is effective for fiscal years 
beginning after December 15, 1997. Reclassification of financial statements 
for earlier periods is required for comparative purposes.  The Company does 
not  believe that this will have a material impact on results of operations.  

                                      13




                                      PART II.
                                           
                                  OTHER INFORMATION
                                           
                                           

Item 1.  Legal Proceedings:
         ------------------

         None

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 and Development Agreement between the Company and Kissei
              Pharmaceutical Co. Ltd  and the Company effective September 10,
              1997 (filed herewith with certain confidential information
              deleted).
         
         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


                                      14


 
                                      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 12, 1997               /s/ Thomas G. Auchincloss, Jr.     
                                       ---------------------------------------
                                       Thomas G. Auchincloss, Jr.
                                       Vice President of Finance and Treasurer
                                       (Principal Financial Officer)



Date:  November 12, 1997               /s/ Hans D. van Houte    
                                       ---------------------------------------
                                       Hans D. van Houte
                                       Controller
                                       (Principal Accounting Officer)
 

                                      15