UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                    FORM 10-Q


X    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 1998.

                                       OR

     TRANSITION  REPORT  PURSUANT  TO  SECTION  13 OR  15(d)  OF THE  SECURITIES
     EXCHANGE  ACT OF  1934  FOR  THE  TRANSITION  PERIOD  FROM  ___________  TO
     ___________.


                         Commission File Number 0-22570


                             Lynx Therapeutics, Inc.
             (Exact name of registrant as specified in its charter)

            Delaware                                             94-3161073
(State or other jurisdiction of                              (I.R.S. Employer
 incorporation or organization)                             Identification No.)


        3832 Bay Center Place
             Hayward, CA                                             94545
(Address of principal executive offices)                          (Zip Code)


                                 (510) 670-9300
              (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   

The  number of shares of Common  Stock  outstanding  as of April 30,  1998,  was
11,099,718.  The  aggregate  market value of the common stock of the  Registrant
held by non-affiliates as of April 30, 1998 was $87,186,929.

                                                                    Page 1 of 13




                             Lynx Therapeutics, Inc.


                                      INDEX


PART I      FINANCIAL INFORMATION                                           Page
                                                                            ----

Item 1.     Condensed Consolidated Balance Sheets - March 31, 1998
                and December 31, 1997........................................ 3

            Condensed Consolidated Statements of Operations - three months
                 ended March 31, 1998 and 1997............................... 4

            Condensed Consolidated Statements of Cash Flows - three months
                ended March 31, 1998 and 1997................................ 5

            Notes to Condensed Consolidated Financial Statements............. 6

Item 2.     Management's Discussion and Analysis of
                Financial Condition and Results of Operations................ 8


PART II     OTHER INFORMATION

Item 1.     Legal Proceedings................................................10

Item 2.     Changes in Securities............................................10

Item 3.     Defaults Upon Senior Securities..................................10

Item 4.     Submission of Matters to a Vote of Security Holders..............10

Item 5.     Other Information................................................10

Item 6.     Exhibits and Reports on Form 8-K.................................10

Signatures  .................................................................11

                                                                    Page 2 of 13




PART I            FINANCIAL INFORMATION
Item 1.           Financial Statements


                                                       Lynx Therapeutics, Inc.
                                                CONDENSED CONSOLIDATED BALANCE SHEETS
                                                           (In thousands)


                                                                                                    March 31,           December 31,
                                                                                                      1998                  1997*
                                                                                                    -------------------------------
                                                                                                   (Unaudited)
                                                                                                                          
Assets
Current assets:
   Cash and cash equivalents                                                                        $ 15,379               $  8,798
   Short-term investments                                                                              8,720                 16,132
   Accounts receivable                                                                                   350                    244
   Other current assets                                                                                  163                    199
                                                                                                    -------------------------------
Total current assets                                                                                  24,612                 25,373

Property and equipment:
   Leasehold improvements                                                                              3,803                  3,795
   Laboratory and other equipment                                                                      2,807                  3,562
                                                                                                    -------------------------------
                                                                                                       6,610                  7,357
   Less accumulated depreciation and amortization                                                     (2,709)                (3,588)
                                                                                                    -------------------------------
Net property and equipment                                                                             3,901                  3,769

Notes receivable from employees                                                                           49                    125
Long-term investments                                                                                  1,747                   --
                                                                                                    -------------------------------
                                                                                                    $ 30,309               $ 29,267
                                                                                                    ===============================
Liabilities and stockholders' equity
Current liabilities:
   Accounts payable                                                                                 $  1,299               $    210
   Accrued compensation                                                                                  177                    289
   Accrued professional fees                                                                             151                    179
   Deferred revenue from related parties                                                               1,604                  2,292
   Other accrued liabilities                                                                             437                    528
                                                                                                    -------------------------------
Total current liabilities                                                                              3,668                  3,498

Other noncurrent liabilities                                                                             187                    179

Stockholders' equity:
   Preferred stock                                                                                      --                   27,189
   Common stock                                                                                       74,357                 46,640
   Notes receivable from stockholders                                                                   (460)                  (460)
   Deferred compensation                                                                              (5,064)                (5,394)
   Accumulated other comprehensive income (loss)                                                         (31)                   (45)
   Accumulated deficit                                                                               (42,348)               (42,340)
                                                                                                    -------------------------------
Total stockholders' equity                                                                            26,454                 25,590
                                                                                                    ===============================
                                                                                                    $ 30,309               $ 29,267
                                                                                                    ===============================

<FN>
*    The Balance  Sheet  amounts at December 31, 1997 have been derived from audited  financial  statements  at that date but do not
     include all of the  information  and footnotes  required by generally  accepted  accounting  principles for complete  financial
     statements.

                                                       See accompanying notes.
</FN>

                                                                                                                        Page 3 of 13






                             Lynx Therapeutics, Inc.
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                    (In thousands, except per share amounts)
                                   (Unaudited)


                                                            Three Months Ended
                                                                March 31,
                                                           --------------------
                                                             1998         1997
                                                           -------      -------

 Net revenues:
    Revenues from collaborative arrangements with          $   688      $ 1,063
    related parties
    Other revenues                                             126           72
                                                           --------------------
 Total revenues                                                814        1,135

 Operating  expenses:
    Research and development                                 3,842        3,075
    General and administrative                                 492          425
                                                           --------------------
 Total operating  expenses                                   4,334        3,500
                                                           --------------------

 Loss from operations                                       (3,520)      (2,365)

 Interest income                                               336          171
 Gain on sale of Antisense Business                          3,176         --
                                                           --------------------
 Net loss                                                  $    (8)     $(2,194)
                                                           ====================

 Basic and diluted net loss per share                      $ (0.00)     $ (0.80)
                                                           ====================

 Shares used in per share computation                        5,729        2,759
                                                           ====================

                             See accompanying notes.

                                                                    Page 4 of 13





                                                       Lynx Therapeutics, Inc.
                                           CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                                           (In thousands)
                                                             (Unaudited)


                                                                                                           Three Months Ended
                                                                                                                March 31,
                                                                                                        ---------------------------
                                                                                                          1998               1997
                                                                                                        --------           --------
                                                                                                                           
Cash flows from operating activities
Net loss                                                                                                $     (8)          $ (2,194)
Adjustments to reconcile net loss to net cash used in operating activities:
     Depreciation and amortization                                                                           355                300
     Amortization of deferred compensation                                                                   330                180
     Non-cash consideration received and costs incurred on the sale of the
       Antisense Business, net                                                                              (417)              --
     Changes in operating assets and liabilities:
         Accounts receivable                                                                                (106)                46
         Other current assets                                                                                 36                 67
         Accounts payable                                                                                  1,089                 74
         Accrued liabilities                                                                                (231)              (191)
         Deferred revenue from related party                                                                (688)            (1,063)
         Other noncurrent liabilities                                                                          8                  8
                                                                                                        ---------------------------
Net cash provided by (used in) operating activities                                                          368             (2,773)

Cash flows from investing activities
Purchases of short-term investments                                                                       (5,667)              --
Maturities of short-term investments                                                                      13,093              1,975
Purchases of long-term investments                                                                          (865)              --
Purchases of property and equipment                                                                         (697)              (865)
Notes receivable from employees                                                                               (9)                (5)
                                                                                                        ---------------------------
Net cash provided by investing activities                                                                  5,855              1,105

Cash flows from financing activities
Issuance (repurchase) of common stock                                                                        358                (32)
                                                                                                        ---------------------------
Net cash provided by (used in) financing activities                                                          358                (32)
                                                                                                        ---------------------------

Net increase (decrease) in cash and cash equivalents                                                       6,581             (1,700)
Cash and cash equivalents at beginning of period                                                           8,798             12,109
                                                                                                        ---------------------------
Cash and cash equivalents at end of period                                                              $ 15,379           $ 10,409
                                                                                                        ===========================

<FN>
                                                       See accompanying notes.
</FN>

                                                                                                                        Page 5 of 13






                             Lynx Therapeutics, Inc.
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

                                 March 31, 1998
                                   (Unaudited)


1.       Ownership and Nature of Business

         Lynx Therapeutics,  Inc. ("Lynx" or the "Company"), was incorporated in
February  1992 under the laws of the State of Delaware.  Lynx has spent the last
several years developing unique, proprietary technologies designed to enable the
simultaneous  identification  and  analysis  of all  (or  nearly  all)  the  DNA
molecules or fragments in a single  biological  sample.  Utilizing its massively
parallel solid phase  cloning,  massively  parallel  hybridization  arrays,  and
massively parallel sequencing technologies, Lynx expects eventually to probe for
genetic and genomic  information  in a much more  efficient  manner than current
technologies.   The  proposed   applications   of  Lynx's   massively   parallel
technologies  include gene discovery,  gene expression,  high resolution  genome
mapping  and  the  identification  of  genetic  variations.   Lynx  expects  its
technologies will be applicable to the genomes of man, pathogenic organisms, and
commercially  important plants and animals.  Lynx believes that its technologies
will open new avenues to understanding  genetics and the  relationships  between
gene function and the various states from health to disease.

2.       Basis of Presentation

         The accompanying  condensed  consolidated financial statements included
herein have been prepared by the Company  without  audit,  pursuant to the rules
and  regulations  promulgated  by the Securities  and Exchange  Commission  (the
"Commission"). Certain prior year amounts have been reclassified to conform with
current year presentation. Certain information and footnote disclosures normally
included in financial  statements prepared in accordance with generally accepted
accounting  principles  have  been  omitted  pursuant  to  Commission  rules and
regulations;  nevertheless,  the  Company  believes  that  the  disclosures  are
adequate to make the  information  presented not  misleading.  In the opinion of
management, the financial statements contain all adjustments, consisting only of
normal  recurring  adjustments,   necessary  to  present  fairly  the  financial
position,  results of  operations  and cash flows of the Company for the interim
periods  presented.  The results of  operations  for the quarter ended March 31,
1998, are not necessarily indicative of the results for the full year.

         The unaudited condensed  consolidated  financial statements include all
accounts of the Company and its wholly owned subsidiary, Lynx GmbH, formed under
the laws of the  Federal  Republic  of  Germany.  All  significant  intercompany
balances have been eliminated.

         These  financial  statements  should  be read in  conjunction  with the
audited  consolidated  financial  statements and notes thereto for the Company's
year ended  December 31, 1997,  included in its annual report on Form 10-K filed
with the Securities and Exchange Commission.

3.       Summary of Significant Accounting Policies

Net Loss Per Share

         In 1997,  the Financial  Accounting  Standards  Board  ("FASB")  issued
Statement of Financial  Accounting Standards No. 128 ("SFAS" 128), "Earnings Per
Share"  ("EPS"),  effective for periods ending after December 15, 1997. SFAS 128
requires that  companies  present two measures of earnings per share,  basic and
diluted.

         Basic  loss per share is  calculated  by  dividing  net  income or loss
applicable  to common  shareholders  by the  weighted  average  number of common
shares  outstanding,  net of certain common shares outstanding which are subject
to continued  vesting and the Company's  right of repurchase,  while diluted EPS
reflects the potential  dilution of securities  that could share in the earnings
of the company,  to the extent such  securities are dilutive.  Basic and diluted
loss per  share are  equivalent  for all  periods  presented  herein  due to the
Company's  net loss.  The Company  has  adopted  SFAS 128 for annual and interim
financial  statements  issued after  December 15, 1997,  and has  calculated and
restated  EPS in  accordance  with  SFAS 128 for each  period in which an income
statement is reported.  The following have been excluded from the calculation of
loss  per  share  because  the  effect  of  inclusion  would  be   antidilutive:
approximately 270,000 common shares which are outstanding but are subject to the
Company's right of repurchase which expires ratably over 5 years, and options to
purchase  approximately  1,400,000  shares of common stock at a weighted average
price of $4.67 per share.  Additionally,  all  periods  prior to March 31,  1998

                                                                    Page 6 of 13




exclude approximately 500,000 shares of Series B, C, and D convertible preferred
stock.  On March 31, 1998,  the preferred  stock  converted to common stock on a
ten-for-one  basis.  The  converted  shares  are,  and will be,  included in the
calculations of basic EPS in all periods including, and subsequent to, March 31,
1998. (See Note 5)

Comprehensive Income

         As of January 1, 1998,  the  Company  adopted  Statement  of  Financial
Accounting  Standards,  No. 130 ("SFAS  130"),  Comprehensive  Income.  SFAS 130
establishes new rules for the reporting and display of comprehensive  income and
its components.  SFAS 130 requires  unrealized  gains or losses on the Company's
available-for-sale  securities, which prior to adoption were reported separately
in shareholders'  equity, to be included in other  comprehensive  income.  Prior
year financial  statements have been reclassified to conform to the requirements
of SFAS 130.

         During the first  quarter of 1998 and 1997,  total  comprehensive  loss
amounted to $39,000 and $2.2 million, respectively.

4.       Sale of the Antisense Business

         On  March  10,  1998,  Lynx  sold  its  portfolio  of  phosphorothioate
antisense   patents   and   licenses,   and  its   therapeutic   oligonucleotide
manufacturing  facility  (collectively,   the  "Antisense  Business"),  to  Inex
Pharmaceuticals   Corporation   ("Inex")   a   Canadian   company.   As  partial
consideration  in this  transaction,  Lynx  received $3 million in cash and will
receive 1.2 million  shares of Inex common stock,  in three equal  installments,
with the first  400,000  shares  received on the above date,  and the second and
third  installments  of stock to be received no later than two and three  years,
respectively,  from the closing date of the  transaction.  The Inex common stock
received  by Lynx is subject to certain  restrictions  on trading  for  specific
periods of time  following  receipt by Lynx.  Lynx is also  entitled  to receive
royalties on future sales of phosphorothioate  antisense products.  In addition,
Lynx has agreed to a  royalty-bearing  license to Inex for its  phosphoroamidate
chemistry  for  certain  therapeutic  applications  in the  fields of cancer and
inflammation that will be defined later.

         The gain on the sale of the Antisense Business is based on the cash and
the first installment of the Inex common stock received on the transaction date,
net of the book value of the assets  transferred to Inex and certain other costs
associated  with the  transaction and incurred by Lynx. The Inex common stock is
classified in long term assets.

5.        Conversion of Preferred Stock to Common Stock

         On March 31, 1998, pursuant to the Amended and Restated  Certificate of
Designation  dated  September 30, 1997, all of the shares of Series B, Series C,
and Series D preferred  stock were  converted into common stock on a ten-for-one
basis.  The inclusion of these shares in both the basic and diluted earnings per
share will have a  significant  impact on the earnings per share amounts in 1998
and  subsequent  years.  The net loss per share for the quarter ending March 31,
1998,  would have been  $(0.00) if the Series B, Series C and Series D preferred
stock were converted to common stock on January 1, 1998.

6.       New Facility Lease

         On February 27, 1998, the Company  entered into a  noncancelable  lease
for additional facilities space. The term of the lease commences on December 15,
1998 and expires on December 14, 2008. Under the terms of the lease, the monthly
rental  payments are fixed for the first  twenty-four  months.  Thereafter,  the
monthly  rental  payments  increase,  and are subject to annual  Consumer  Price
Index-based  adjustments,  with minimum and maximum limits.  The Company has the
option  to extend  the lease for an  additional  five year  period,  subject  to
certain  conditions,  with payments to be determined at the time of the exercise
of  such  option.  Additionally,  the  Company  has an  option  (the  "Expansion
Option"),  exercisable  on or prior to  January  1,  2000,  to lease  additional
building space for expansion  purposes.  In return for the Expansion Option, the
Company  may be  subject to a nominal  carrying  cost on the  additional  space,
depending on the timing of the exercise of such option, if ever.

                                                                    Page 7 of 13




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

         Except for the historical  information  contained herein, the following
discussion   contains   forward-looking   statements   that  involve  risks  and
uncertainties.  The Company's actual results could differ  materially from those
discussed  here.  Factors  that could cause or  contribute  to such  differences
include,  but are not limited to, those discussed in this section, as well as in
the Company's  annual report (Form 10-K) filed with the  Securities and Exchange
Commission for the fiscal year ended December 31, 1997.

Overview

Results of Operations

Revenue

         Revenue was $0.8 million and $1.1 million for the quarters  ended March
31, 1998 and 1997, respectively.  Revenues for 1998 included $0.7 million earned
under a collaborative  agreement with BASF AG ("BASF"),  and approximately  $0.1
million in other revenue,  primarily  compound for use in clinical  trials.  The
1997  revenues  included $0.7 million from BASF and $0.4 million from Hoechst AG
and Hoechst Marion Roussel (collectively,  "Hoechst") earned under collaborative
agreements.  Revenue will  continue to fluctuate  based on activity with current
and potential corporate partners and achievement of milestones.

Operating Expenses

         Research and development expenses were $3.8 million and $3.1 million in
the quarters ended March 31, 1998 and 1997,  respectively.  The increase was due
to  the  building  of  production   capacity  for  the  anticipated   commercial
application of the Company's novel, proprietary massively parallel technologies,
and to higher  amortization  of  deferred  compensation  related to the grant of
stock options, partially offset by reduced funding to various laboratories under
collaborative  research  agreements.  Lynx  expects  to  incur  substantial  and
increasing research and development expenses due to planned spending for ongoing
technology development and implementation, and new research applications.

         General and administrative expenses were $492,000 for the quarter ended
March 31, 1998,  compared to $425,000 for the quarter ended March 31, 1997.  The
increase was due to higher headcount-related  expenses. Lynx expects to continue
to incur  substantial  administrative  expenses in support of its  research  and
development efforts.

Interest Income

         Interest  income was $336,000 and $171,000 for the quarters ended March
31, 1998 and 1997  respectively.  The increase was due to a higher  average cash
balance in the quarter ended March 31, 1998 than in the same quarter in 1997.

Gain on Sale of Antisense Business

         Other income of $3.2  million for the quarter  ended March 31, 1998 was
comprised  of the  gain on the  sale of  Lynx's  portfolio  of  phosphorothioate
antisense   patents   and   licenses,   and  its   therapeutic   oligonucleotide
manufacturing  facility   (collectively,   the  "Antisense  Business")  to  Inex
Pharmaceuticals   Corporation   ("Inex").   As  partial  consideration  in  this
transaction,  Lynx  received  $3 million in cash and will  receive  1.2  million
shares of Inex common stock, in three equal installments, with the first 400,000
shares  received on March 10,  1998,  and the second and third  installments  of
stock to be received no later than two and three years,  respectively,  from the
closing  date of the  transaction.  The Inex  common  stock  received by Lynx is
subject  to  certain  restrictions  on  trading  for  specific  periods  of time
following receipt by Lynx.

         The gain on the sale of the Antisense Business reflects on the cash and
the first installment of the Inex common stock received on the transaction date,
net of the book value of the assets  transferred to Inex and certain other costs
associated with the transaction and incurred by Lynx.

                                                                    Page 8 of 13




Liquidity and Capital Resources

         Net cash  provided by operating  activities of $367,000 for the quarter
ended March 31,  1998,  differed  from the net loss for the same period in 1997,
primarily due to increases in payables,  the non-cash consideration received and
costs incurred on the sale of the Antisense Business, current period recognition
of a portion of previously deferred revenue, depreciation and amortization,  and
deferred compensation expense. Net cash provided by investing activities related
to maturities of short-term investments partially offset by purchases of capital
equipment.  Net cash provided by financing activities related to the exercise of
stock options by employees. Cash and equivalents were $15.4 million at March 31,
1998.

         Lynx   plans  to  use   available   funds  for  the   development   and
implementation of its massively parallel  technologies and to build capacity for
their early commercial uses.  Pending such uses as described above, Lynx intends
to invest its excess  cash in  short-term,  investment  grade,  interest-bearing
securities or certificates of deposit.

         Since  commencing  operations  as  an  independent  company,  Lynx  has
obtained funding for its operations  through sales of preferred and common stock
to  venture  capital  investors,   institutional  investors,  and  collaborative
partners;  revenue from  collaborative  research and  development  arrangements,
interest income,  product sales, and government  grants.  The cost,  timing, and
amount  of  funds  required  for  specific  uses by  Lynx  cannot  be  precisely
determined  at this time and will be based upon Lynx's  progress in its research
and development,  administrative and legal costs, the establishment of corporate
collaborations and other arrangements, and the availability of alternate methods
of financing.

         Lynx  expects  to  incur   substantial  and  increasing   research  and
development  expenses  and  intends  to seek  additional  financing,  as needed,
through  contractual  arrangements  with  corporate  partners and equity or debt
offerings.  There can be no assurance that any additional  financing required by
Lynx will be available or, if available, will be on terms favorable to Lynx. The
Company  believes  that,  at  current  spending  levels,  its  existing  capital
resources and interest income thereon will enable it to maintain its current and
planned operations at least through mid-1999.

Impact of Year 2000

         The Company has  completed  an  assessment  of its  computer  operating
systems and related  software and, with only a few minor  exceptions,  has found
them to be Year 2000  compliant.  The  Company's  exposure is limited due to the
fact that most of its computers and software were acquired  within the past five
years and were Year 2000 compliant at purchase. The Company plans to replace the
operating  systems on the few  non-compliant  computers  before 2000 and expects
that the  cost  will be  immaterial.  The  Company  believes  that  even if such
modifications  are not made,  there  will be no  adverse  impact on  operations.
However,  Year 2000  problems may affect the computer  systems of the  Company's
business partners,  vendors, customers, and financial service organizations with
which the Company interacts.  The Company is in the process of developing a plan
to determine the impact that third parties which are not Year 2000 compliant may
have on the operations of the Company.  There can be no assurance that such plan
will be able to address fully, or at all, the "Year 2000 issue" which could have
a material adverse effect upon the Company's  business, financial  condition and
results of operations.

                                                                    Page 9 of 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 and Reports on Form 8-K.

                      a)  Exhibits  -  The  following  documents  are  filed  as
Exhibits to this report:

                           Exhibit
                           Number         Description
                           ------         -----------

                           10.35*         Lease,  dated as of February 27, 1998,
                                          between the Company and SimFirst, L.P.
                                          limited partnership

                           27.1           Financial Data Schedule


                          *Portions of this agreement have been deleted pursuant
                           to our request for confidential treatment.

                      b)   The  Company  filed a  Current  Report on Form 8-K on
                           March  24,  1998,  reporting  under  Item 2 that  the
                           Company had sold its  portfolio  of  phosphorothioate
                           antisense  patents and licenses,  and its therapeutic
                           oligonucleotide   manufacturing   facility,  to  Inex
                           Pharmaceuticals Corporation of Vancouver, Canada.

                                                                   Page 10 of 13




                                   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.


                                            LYNX THERAPEUTICS, INC.

                                            /s/  Sam Eletr
                                            ------------------------------------
                                            By:      Sam Eletr, Ph.D.
                                                     Chief Executive Officer and
                                                     Chairman of the Board
                                            Date:    May 13, 1998


                                            /s/  Edward C. Albini
                                            ------------------------------------
                                            By:      Edward C. Albini
                                                     Chief Financial Officer
                                                     (Principal Financial and
                                                     Accounting Officer)
                                            Date:    May 13, 1998

                                                                   Page 11 of 13