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 June 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                  25,096,445
- --------------------------------------            ------------------------
         Class                                   Outstanding at August 5, 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 -
            June 30, 1997 and December 31, 1996                      4

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

          Condensed Consolidated Statements of Operations -
            Six Months Ended June 30, 1997 and 1996                  6

          Condensed Consolidated Statements of Cash Flows -
            Six Months Ended June 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                        9

Part II. -  Other Information                                       13

Signatures                                                          14

                                    2



 
                     REPORT OF INDEPENDENT ACCOUNTANTS
 
To the Board of Directors and Stockholders of Vertex Pharmaceuticals 
Incorporated:
 
We have reviewed the accompanying condensed balance sheet of Vertex
Pharmaceuticals Incorporated as of June 30, 1997, and the related condensed
consolidated statements of operations and cash flows for the three-month and the
six-month periods then ended. 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 accompanying financial statements for them to be in
conformity with generally accepted accounting principles. 

                                          /s/ COOPERS & LYBRAND L.L.P.
 
Boston, Massachusetts
July 22, 1997
 
                                       3



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


                                                                                          JUNE 30,   DECEMBER 31,
                                                                                            1997         1996
                                                                                         ----------  ------------
                                                                                               
ASSETS
Current assets:
   Cash and cash equivalents...........................................................  $  188,584   $   34,851
   Short-term investments..............................................................      97,582       95,508
   Prepaid expenses and other current assets...........................................       1,642        1,791
                                                                                         ----------  ------------
      Total current assets.............................................................     287,808      132,150
Restricted cash........................................................................       2,316        2,316
Property and equipment, net............................................................      10,007        8,663
Other assets...........................................................................         535          370
                                                                                         ----------  ------------
      Total assets.....................................................................  $  300,666   $  143,499
                                                                                         ----------  ------------
                                                                                         ----------  ------------
                 LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
   Obligations under capital lease.....................................................  $    2,815   $    2,910
   Accounts payable and accrued expenses...............................................       5,397        4,146
   Deferred revenue....................................................................       1,056       --
                                                                                         ----------  ------------
      Total current liabilities........................................................       9,268        7,056
                                                                                         ----------  ------------
Obligations under capital leases, excluding 
   current portion.....................................................................       5,446        5,617
                                                                                         ----------  ------------
      Total liabilities................................................................      14,714       12,673
                                                                                         ----------  ------------
Stockholders' equity:
   Common stock........................................................................         251          211
   Additional paid-in capital..........................................................     389,822      227,510
   Equity adjustments..................................................................           1           49
   Accumulated deficit.................................................................    (104,122)     (96,944)
                                                                                         ----------  ------------
      Total stockholders' equity.......................................................     285,952      130,826
                                                                                         ----------  ------------
      Total liabilities and stockholders' equity.......................................  $  300,666   $  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 JUNE 30,
                                                           ---------------------------
                                                                 1997          1996
                                                              ---------    ----------
                                                                   

Revenues:
   Collaborative and other research and development........  $   8,320    $  3,116
   Interest income.........................................      3,835       1,030
                                                              ---------  ----------
     Total revenues........................................     12,155       4,146
                                                              ---------  ----------
Costs and expenses:
   Research and development................................     10,798       9,490
   General and administrative..............................      2,624       1,878
   License payment.........................................      --         15,000
   Interest................................................        145         103
                                                            ------------   ------------

     Total costs and expenses..............................     13,567      26,471
                                                            ------------  ------------
Net loss...................................................  $  (1,412) $  (22,325)
                                                            ------------  ------------
                                                            ------------  ------------
Net loss per common share..................................  $   (0.06) $    (1.28)
                                                            ------------  ------------
                                                            ------------  ------------
Weighted average number of common shares 
   outstanding.............................................     24,722       17,398
                                                            ------------  ------------
                                                            ------------  ------------

 
             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)
 


                                                                                             SIX MONTHS ENDED JUNE 30,
                                                                                             -------------------------
                                                                                                  
                                                                                               1997        1996
                                                                                             ---------  ----------
Revenues:
   Collaborative and other research and development........................................  $  12,980  $    5,589
   Interest income.........................................................................      6,093       2,308
                                                                                             ---------  ----------
Total revenues.............................................................................     19,073       7,897
                                                                                             ---------  ----------
Costs and expenses:
   Research and development................................................................     21,112      18,827
   General and administrative..............................................................      4,841       3,641
   License payment.........................................................................     --          15,000
   Interest................................................................................        298         222
                                                                                             ---------  ----------
     Total costs and expenses..............................................................     26,251      37,690
                                                                                             ---------  ----------
Net loss...................................................................................  $  (7,178) $  (29,793)
                                                                                             ---------  ----------
                                                                                             ---------  ----------
Net loss per common share..................................................................  $   (0.31) $    (1.72)
                                                                                             ---------  ----------
                                                                                             ---------  ----------
Weighted average number of common shares 
   outstanding.............................................................................     23,356      17,365
                                                                                             ---------  ----------
                                                                                             ---------  ----------

 
                      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)
 


                                                                                  SIX MONTHS ENDED JUNE 30,
                                                                                  -------------------------
                                                                                        
                                                                                   1997           1996
                                                                                  -----           ----
Cash flows from operating activities:
  Net loss....................................................................... $(7,178)    $  (29,793)
  Adjustments to reconcile net loss to 
    net cash used by operating activities:
     Depreciation and amortization...............................................   1,644           1,675
     Changes in assets and liabilities:
      Prepaid expenses and other 
        current assets...........................................................     149           (789)
      Accounts payable and accrued 
        expenses.................................................................   1,251         (2,380)
      Deferred revenue...........................................................   1,056             803
                                                                                  -------        --------
        Net cash provided (used) by 
            operating activities................................................. (3,078)        (30,484)
                                                                                  -------        --------
Cash flows from investing activities:
   Net purchases and sales of short-term investments............................. (2,116)           7,080
   Expenditures for property and equipment....................................... (2,988)         (1,057)
   Other assets..................................................................   (165)         (1,085)
                                                                                  -------         -------
      Net cash provided (used) by investing          
        activities............................................................... (5,269)           4,938
                                                                                  -------         -------
Cash flows from financing activities:
   Net proceeds from public offering of common stock............................. 148,810              --
   Proceeds from private placement of common stock...............................  10,000           5,000
   Other issuances of common stock...............................................   3,542           1,536
   Proceeds from equipment sale/leaseback........................................   1,179             903
   Repayment of capital lease obligations........................................ (1,445)         (1,034)
                                                                                  ------          -------
      Net cash provided (used) by 
       financing activities...................................................... 162,086           6,405
                                                                                  -------         -------

Effect of exchange rate changes on cash..........................................     (6)               1
                                                                                  -------         -------
Increase (decrease) in cash and cash equivalents................................. 153,733        (19,140)
Cash and cash equivalents at beginning of period.................................  34,851          28,390
                                                                                  -------        --------
Cash and cash equivalents at end of period.......................................$188,584        $  9,250
                                                                                 --------       ---------
                                                                                 --------       ---------

 
                       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, but does not include all disclosures required by 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 June 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. COLLABORATIVE AGREEMENT WITH ELI LILLY AND COMPANY
 
    In June 1997, Vertex and Eli Lilly and Company ("Lilly") entered into a 
collaborative agreement for the research, development and commercialization 
of novel, small molecule compounds 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 initial 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.
 
               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, hemoglobin disorders, autoimmune diseases, inflammatory
diseases and neurodegenerative disorders. Five of these programs are in the
development phase, and the other four are in the research phase. During the
second quarter of 1997, Vertex's partner, Glaxo Wellcome plc ("Glaxo Wellcome"),
advanced Phase II and 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 Pharmaceutical Co., Ltd. ("Kissei") is also developing VX-478 as
Vertex's partner for the HIV program in the Far East. Through a series of Phase
II clinical trials underway or planned, Vertex and its partner for development
and marketing of VX-710 in Canada, BioChem Therapeutics Inc. ("BioChem"), are
evaluating VX-710 to reverse cancer multidrug resistance in solid tumors. In
addition, Vertex signed a research, development and commercialization agreement
with Eli Lilly and Company ("Lilly") to develop new drugs to treat hepatitis C
infection.
 
    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.
 
                                       9



                      VERTEX PHARMACEUTICALS INCORPORATED

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

RESULTS OF OPERATIONS
 
    Three Months Ended June 30, 1997 Compared with Three Months Ended June 
30, 1996. For the second quarter of 1997, the Company's total revenues were 
$12,155,000 as compared to $4,146,000 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 second 
quarter of 1997, the Company received $7,822,000 in revenue from its 
collaborative agreements, $3,835,000 in interest received on invested funds 
and $498,000 from government grants and other revenue. In the second quarter 
of 1996, the Company received $2,715,000 in revenue from its collaborative 
agreements, $1,030,000 in interest received on invested funds and $401,000 
from government grants and other revenue. The increase in revenue for the 
second quarter in 1997 is attributable to greater collaborative revenue and 
interest income on higher levels of cash and short-term investments. 
Collaborative revenue in the second quarter of 1997 included a $3,000,000 
up-front payment and approximately $190,000 in research funding for the 
Company's hepatitis C program received from Lilly under the collaborative 
agreement signed in June 1997. In addition, the Company received a $2,000,000 
payment from Kissei for reimbursement of costs associated with an ongoing 
Phase II clinical trial of Vertex's HIV protease inhibitor, VX-478, as 
single-drug therapy for HIV infection. Also during the second quarter of 
1997, Ciba Geigy Limited exercised a development option resulting in a 
milestone payment of $200,000 and research revenue of $200,000 pursuant to a 
collaboration with the Company's subsidiary, Altus Biologics Inc. ("Altus") 
in the field of detergents.
 
    The Company's total costs and expenses decreased to $13,567,000 in the
second quarter of 1997, from $26,471,000 during the same period in 1996. During
the second quarter in 1996, the Company made a one-time payment of $15,000,000
to obtain a non-exclusive, worldwide license under certain G.D. Searle & Co.
("Searle") patent applications claiming HIV protease inhibitors. Research and
development expenses were $10,798,000 in the second quarter of 1997 as compared
to $9,490,000 during the same period in 1996. This increase in cost is
principally a result of the continued growth of the Company's research and
development organization and increasing expenditures for the preclinical
development of VX-497, the Company's lead candidate in its IMPDH program for
potential new therapies for autoimmune diseases and also increased costs
associated with expanded Phase II clinical trials of VX-710, the Company's lead
compound in the multidrug resistance program. General and administrative
expenses increased during the second quarter of 1997 to $2,624,000 from
$1,878,000 in the second 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 Altus. Interest
expense increased to $145,000 in the second quarter of 1997 as compared to
$103,000 during the same period in 1996 due to higher levels of equipment
financing.
 
    The Company incurred a net loss of $1,412,000 or $0.06 per share in the
second quarter of 1997 as compared to a net loss of $22,325,000 or $1.28 per
share in the second quarter of 1996.
 
                                       10




                      VERTEX PHARMACEUTICALS INCORPORATED

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


    Six Months Ended June 30, 1997 Compared with Six Months Ended June 30, 
1996. The Company's total revenues increased to $19,073,000 for the six 
months ended June 30, 1997 from $7,897,000 for the six months ended June 30, 
1996. In 1997, the Company's revenues consisted of $12,059,000 earned under 
the Company's collaborative agreements, $6,093,000 in interest income and 
$921,000 in government grants and other income. The Company's revenues during 
the same period in 1996, consisted of $5,147,000 earned under the Company's 
collaborative agreements, $2,308,000 in interest income and $442,000 in 
government grants and other income. The increase in revenue for the first 
half of 1997 compared to the same period in 1996 was principally due to the 
up-front payment of $3,000,000 by Lilly upon the commencement of the 
hepatitis C collaboration, $4,000,000 in development reimbursements from 
Kissei for an ongoing clinical trial of Vertex's HIV protease inhibitor, and 
increased investment income from higher levels of cash and investments due to 
the successful completion of public offerings of the Company's stock in 
August 1996 and March 1997. 

    The Company's total costs decreased to $26,251,000 for the six months 
ended June 30, 1997 from $37,690,000 for the six months ended June 30, 1996. 
The Company paid $15,000,000 in the first half of 1996 to obtain a 
non-exclusive, worldwide license under certain Searle patent applications 
claiming HIV protease inhibitors. Research and development expenses increased 
to $21,112,000 in the first half of 1997 from $18,827,000 in the first half 
of 1996, primarily due to additional scientific staffing as well as the 
commencement of preclinical activities for VX-497, the lead compound in the 
Company's IMPDH program. 

    General and administrative expenses increased during the first half of 
1997 to $4,841,000 from $3,641,000 in the first half 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 
Altus. Interest expense was $298,000 in the second half of 1997, an increase 
from $222,000 in the second half 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 $7,178,000
or $0.31 per share in the six months ended June 30, 1997 compared to a net loss
of $29,793,000 or $1.72 per share in the six months ended June 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, 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.

                                       11



                      VERTEX PHARMACEUTICALS INCORPORATED

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

 
    The Company expects to finance these substantial cash needs with its
existing cash and investments at June 30, 1997 of approximately $286 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 June 1997, the Company entered into a collaborative agreement for up to
$51 million with Lilly for the research, development and commercialization of
compounds in connection with the Company's hepatitis C program. 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.
 
    The Company's aggregate cash and investments increased by $155,807,000
during the six months ended June 30, 1997 to $286,166,000, principally due to
the public offering 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 $3,078,000 during the same period. The Company also expended
$2,988,000 during this period to acquire property and equipment, principally for
research equipment and facilities. During the first quarter of 1997, the Company
entered into equipment lease financing in the aggregate amount of $1,179,000 and
repaid $1,445,000 of its lease obligations.
 
    In July 1997, the Company purchased a portfolio of ten patent application 
families claiming ICE (interleukin-1 beta converting enzyme) and its 
inhibitors from Sanofi S.A. Through this acquisition, the Company has 
obtained the rights, title and interest to all the patent properties in 
Sanofi's ICE portfolio.
 
    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.
 
                                       12



                                    PART II.
 
                               OTHER INFORMATION
 
ITEM 1. LEGAL PROCEEDINGS:
 
        None
 
ITEM 2. CHANGES IN SECURITIES:
 
        Recent Sales of Unregistered Securities
 
        On June 18, 1997, the Company issued and sold to Lilly, for cash,
        263,922 shares of the Company's Common Stock for an aggregate purchase
        price of $10,000,000. The securities issued were not
        registered under the Securities Act of 1933, as amended (the 
        "Securities Act"), in reliance on the exemption set forth in 
        Section 4(2) of the Securities Act. The sale to Lilly was a privately
        negotiated sale by the Company not involving any public offering.
 
ITEM 3. DEFAULTS UPON SENIOR SECURITIES:
 
        None
 
ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS:
 
        The Company's Annual Meeting of Stockholders was held on May 8, 1997.
        The stockholders elected Charles A. Sanders to the class of directors 
        whose term expires in 1998 and Barry M. Bloom and William W. Helman IV 
        to the class of directors whose term expires in 2000. The tabulation of
        votes with respect to the election of such directors is as follows:
 


                                                                                 TOTAL VOTE        TOTAL VOTE
                                                                                    FOR:           WITHHELD:
                                                                                -------------  ------------------
                                                                                         
Charles A. Sanders............................................................    19,500,766           78,310
Barry M. Bloom................................................................    19,492,781          118,597
William W. Helman IV..........................................................    19,492,981          118,397

 
        The stockholders approved an amendment to the Company's Restated
        Articles of Organization to increase the number of authorized shares of
        Common Stock of the Company from 50,000,000 to 100,000,000 by a vote of
        18,591,245 shares in favor, 979,121 shares against, and 41,012 shares
        abstaining.
 
        A proposal to amend the Company's Restated Articles of Organization to
        increase the number of authorized shares of Preferred Stock from 
        1,000,000 to 5,000,000 was not approved, with 9,304,131 shares voted
        in favor, 6,971,564 shares voted against, 42,442 shares abstaining, and
        3,293,241 broker non-votes.
 
        The stockholders approved the Company's 1996 Stock and Option Plan, with
        9,695,876 shares voted in favor, 6,595,383 shares voted against, 63,262
        shares abstaining, and 3,256,857 broker non-votes.
 
                                       13



        In addition, the stockholders approved the appointment of Coopers &
        Lybrand L.L.P. as the Company's independent accountants for the 1997 
        fiscal year by a vote of 19,548,868 shares in favor, 32,608 shares 
        against, and 29,902 shares abstaining.
 
ITEM 5. OTHER INFORMATION:
 
        None
 
ITEM 6. EXHIBITS:
 
  10.1  Research and Development Agreement between the Company and Eli 
        Lilly and Company effective June 11, 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
 

                            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: August 14, 1997        /s/Thomas G. Auchincloss, Jr. 
                             --------------------------------------
                             Thomas G. Auchincloss, Jr. 
                             Vice President of Finance and Treasurer 
                             (Principal Financial Officer) 

Date: August 14, 1997        /s/Hans D. van Houte 
                             --------------------------------------
                             Hans D. van Houte 
                             Controller 
                             (Principal Accounting Officer)


 
                                       14