QuickLinks -- Click here to rapidly navigate through this document

Exhibit 10.4.1

ABGENIX, INC.

1998 DIRECTOR OPTION PLAN
(As Amended and Restated Effective April 26, 2001)

    1.  Purposes of the Plan.  The purposes of this 1998 Director Option Plan
are to attract and retain the best available personnel for service as Outside
Directors (as defined herein) of the Company, to provide additional incentive to
the Outside Directors of the Company to serve as Directors, and to encourage
their continued service on the Board.

    All options granted hereunder shall be nonstatutory stock options.

    2.  Definitions.  As used herein, the following definitions shall apply:

    (a) "Board" means the Board of Directors of the Company.

    (b) "Code" means the Internal Revenue Code of 1986, as amended.

    (c) "Common Stock" means the Common Stock of the Company.

    (d) "Company" means Abgenix, Inc., a Delaware corporation.

    (e) "Director" means a member of the Board.

    (f)  "Employee" means any person, including officers and Directors, employed
by the Company or any Subsidiary of the Company. Employees of the Parent of the
Company shall not be employees of the Company unless they are also employed by
the Company. The payment of a Director's fee by the Company shall not be
sufficient in and of itself to constitute "employment" by the Company.

    (g) "Exchange Act" means the Securities Exchange Act of 1934, as amended.

    (h) "Fair Market Value" means, as of any date, the value of Common Stock
determined as follows:

     (i) If the Common Stock is listed on any established stock exchange or a
national market system, including with limitation the Nasdaq National Market or
the Nasdaq SmallCap Market of the Nasdaq Stock Market, its Fair Market Value
shall be the closing sales price for such stock (or the closing bid, if no sales
were reported, as quoted on such exchange or system for the market trading day
at the time of determination, or if the determination is not made on a market
trading date, the last market trading day prior to the time of determination) as
reported in The Wall Street Journal or such other source as the Administrator
deems reliable;

    (ii) If the Common Stock is regularly quoted by a recognized securities
dealer but selling prices are not reported, the Fair Market Value of a Share of
Common Stock shall be the mean between the high bid and low asked prices for the
Common Stock on the date of determination, as reported in t) as reported in the
The Wall Street Journal or such other source as the Board deems reliable, or;

    (iii) In the absence of an established market for the Common Stock, the Fair
Market Value thereof shall be determined in good faith by the Board.

    (i)  "Inside Director" means a Director who is an Employee.

    (j)  "New Outside Director" means an Outside Director who becomes a Director
after the effective date of the Plan, as amended and restated.

    (k) "Option" means a stock option granted pursuant to the Plan.

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

    (l)  "Optioned Stock" means the Common Stock subject to an Option.

    (m) "Optionee" means a Director who holds an Option.

    (n) "Outside Director" means a Director who is not an Employee.

    (o) "Parent" means a " parent corporation," whether now or hereafter
existing, as defined in Section 424(e) of the Code.

    (p) "Plan" means this 1998 Director Option Plan.

    (q) "Share" means a share of the Common Stock, as adjusted in accordance
with Section 10 of the Plan.

    (r) "Subsidiary" means a "subsidiary corporation," whether now or hereafter
existing, as defined in Section 424(f) of the Internal Revenue Code of 1986.

    3.  Stock Subject to the Plan.  Subject to the provisions of Section 10 of
the Plan, the maximum aggregate number of shares which may be optioned and sold
under under the Plan is 250,000 Shares of Common Stock (the "Pool"). The Shares
may be authorized, but unissued, or reacquired Common Stock.

    If an Option expires or becomes unexercisable without having been exercised
in full, the unpurchased Shares which were subject thereto shall become
available for future grant or sale under the Plan (unless the Plan has
terminated). Shares that have actually been issued under the Plan shall not be
returned to the Plan and shall not become available for future distribution
under the Plan.

    4.  Administration and Grants of Options under the Plan.  

    (a)  Procedure for Grants.  All grants of Options to Outside Directors under
this Plan shall be automatic and nondiscretionary and shall be made strictly in
accordance with the following provisions:

     (i) No person shall have any discretion to select which Outside Directors
shall be granted Options or to determine the number of Shares to be covered by
Options granted to Outside Directors except as expressly provided by the Plan.

    (ii) Each New Outside Director shall be automatically granted an Option to
purchase that number of Shares as shall be determined by the Board in its sole
discretion (the "First Option") on the date on which such person first becomes
an Outside Director, whether through election by the stockholders of the Company
or appointment by the Board to fill a vacancy; provided, however, that an Inside
Director who ceases to be an Inside Director but who remains a Director shall
not receive a First Option. If the Board does not establish the number of Shares
subject to the First Option for a given New Outside Director prior to the date
of grant for such First Option, then the number shall be the same as the number
of Shares granted to the immediately preceding New Outside Director.

    (iii) Commencing with the fiscal year beginning January 1, 2002, each
Outside Director shall be automatically granted an Option to purchase that
number of Shares as shall be determined by the Board in its sole discretion (a
"Subsequent Option") on the date of the Company's Annual Meeting of Stockholders
upon such Outside Director's reelection, if on such date, he or she shall have
served on the Board for at least six (6) months. If the Board does not establish
the number of Shares subject to the Subsequent Option for a given fiscal year,
then the number shall be the same as the number of Shares subject to the
Subsequent Option for the immediately preceding fiscal year (as adjusted
pursuant to Section 10).

    (iv) Notwithstanding the provisions of subsections (ii) and (iii) hereof,
any exercise of an Option granted before the Company has obtained stockholder
approval of the Shares to be

2

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

issued upon the exercise of such Option shall be conditioned upon obtaining such
stockholder approval.

    (v) The terms of a First Option granted hereunder shall be as follows:

    (A) the maximum term of a First Option shall be ten (10) years.

    (B) the First Option shall be exercisable only while the Outside Director
remains a Director of the Company, except as set forth in Sections 8 and 10
hereof.

    (C) the exercise price per Share shall be 100% of the Fair Market Value per
Share on the date of grant of the First Option. In the event that the date of
grant of the First Option is not a trading day, the exercise price per Share
shall be the Fair Market Value on the next trading day immediately following the
date of grant of the First Option.

    (D) subject to Section 10 hereof, the First Option shall be exercisable
immediately, in whole or in part.

    (vi) The terms of a Subsequent Option granted hereunder shall be as follows:

    (A) the maximum term of the Subsequent Option shall be ten (10) years.

    (B) the Subsequent Option shall be exercisable only while the Outside
Director remains a Director of the Company, except as set forth in Sections 8
and 10 hereof.

    (C) the exercise price per Share shall be 100% of the Fair Market Value per
Share on the date of grant of the Subsequent Option. In the event that the date
of grant of the Subsequent Option is not a trading day, the exercise price per
Share shall be the Fair Market Value on the next trading day immediately
following the date of grant of the Subsequent Option.

    (D) subject to Section 10 hereof, the Subsequent Option shall be exercisable
immediately, in whole or in part.

    (vii) In the event that any Option granted under the Plan would cause the
number of shares subject to outstanding Options plus the number of Shares
previously purchased under Options to exceed the Pool, then the remaining Shares
available for Options grant shall be granted under Options to the Outside
Directors on a pro rata basis. No further grants shall be made until such time,
if any, as additional Shares become available for grant under the Plan through
action of the Board or the stockholders to increase the number of Shares which
may be issued under the Plan or through cancellation or expiration of Options
previously granted hereunder.

    5.  Eligibility.  Options may be granted only to Outside Directors. All
Options shall be automatically granted in accordance with the terms set forth in
Section 4 hereof.

    The Plan shall not confer upon any Optionee any right with respect to
continuation of service as a Director or nomination to serve as a Director, nor
shall it interfere in any way with any rights which the Director or the Company
may have to terminate the Director's relationship with the Company at any time.

    6.  Term of Plan.  The Plan shall become effective upon the earlier to occur
of its adoption by the Board or its approval by the stockholders of the Company
as described in Section 16 of the Plan. It shall continue in effect for a term
of ten (10) years ending in 2008 unless sooner terminated under Section 11 of
the Plan.

    7.  Form of Consideration.  The consideration to be paid for the Shares to
be issued upon exercise of an Option, including the method of payment, shall
consist of (i) cash, (ii) check, (iii) other shares

3

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

which (x) in the case of Shares acquired upon exercise of an Option, have been
owned by the Optionee for more than six (6) months on the date of surrender, and
(y) have a Fair Market Value on the date of surrender equal to the aggregate
exercise price of the Shares as to which said Option shall be exercised,
(iv) delivery of a properly executed notice together with such other
documentation as the Company and the broker, if applicable, shall require to
effect an exercise of the Option and delivery to the Company of the sale or loan
proceeds required to pay the exercise price, or (v) any combination of the
foregoing methods of payment.

    8.  Exercise of Option.  

    (a)  Procedure for Exercise, Rights as a Stockholder.  Any Option granted
hereunder shall be exercisable at such times as are set forth in Section 4
hereof and in accordance with the schedule set forth in the agreement
documenting an individual Option.

    An Option may not be exercised for a fraction of a Share.

    An Option shall be deemed to be exercised when written notice of such
exercise has been given to the Company in accordance with the terms of the
Option by the person entitled to exercise the Option and full payment for the
Shares with respect to which the Option is exercised has been received by the
Company. Full payment may consist of any consideration and method of payment
allowable under Section 7 of the Plan. Until the issuance (as evidenced by the
appropriate entry on the books of the Company or of a duly authorized transfer
agent of the Company) of the stock certificate evidencing such Shares, no right
to vote or receive dividends or any other rights as a stockholder shall exist
with respect to the Optioned Stock, notwithstanding the exercise of the Option.
A share certificate for the number of Shares so acquired shall be issued to the
Optionee as soon as practicable after exercise of the Option. No adjustment
shall be made for a dividend or other right for which the record date is prior
to the date the stock certificate is issued, except as provided in Section 10 of
the Plan.

    Exercise of an Option in any manner shall result in a decrease in the number
of Shares which thereafter may be available, both for purposes of the Plan and
for sale under the Option, by the number of Shares as to which the Option is
exercised.

    (b)  Termination of Continuous Status as a Director.  Subject to Section 10
hereof, in the event an Optionee's status as a Director terminates (other than
upon the Optionee's death or disability), the Optionee may exercise his or her
Option, but only within ninety (90) days following the date of such termination,
and only to the extent that the Optionee was entitled to exercise it on the date
of such termination (but in no event later than the expiration of its ten
(10) year term); provided, however, that in the event that a sale of the Option
Stock received upon exercise of this Option would subject the Director to
liability under Section 16(b) of the Securities and Exchange Act of 1934, as
amended, then the option will terminate on the earlier of (i) fifteenth day
after the last date upon which such sale would result in liability, or (ii) two
hundred ten (210) days following the date of such termination of status as a
Director (but in no event later than the expiration of its ten (10) year term).
To the extent that the Optionee was not entitled to exercise an Option on the
date of such termination, and to the extent that the Optionee does not exercise
such Option (to the extent otherwise so entitled) within the time specified
herein, the Option shall terminate.

    (c)  Disability of Optionee.  In the event Optionee's status as a Director
terminates as a result of disability, the Optionee may exercise his or her
Option, but only within twelve (12) months following the date of such
termination, and only to the extent that the Optionee was entitled to exercise
it on the date of such termination (but in no event later than the expiration of
its ten (10) year term). To the extent that the Optionee was not entitled to
exercise an Option on the date of the time specified herein, the Option shall
terminate.

4

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

    (d)  Death of Optionee.  In the event of an Optionee's death, the Optionee's
estate or a person who acquired the right to exercise the Option by bequest or
inheritance may exercise the Option, but only within twelve (12) months
following the date of death, and only to the extent that the Optionee was
entitled to exercise it on the date of death (but in no event later than the
expiration of its ten (10) year term). To the extent that the Optionee was not
entitled to exercise an Option on the date of death, and to the extent that the
Optionee's estate or a person who acquired the right to exercise such Option
does not exercise such Option (to the extent otherwise so entitled) within the
time specified herein, the Option shall terminate.

    9.  Non-Tranferability of Options.  The Option may not be sold, pledged,
assigned, hypothecated, transferred, or disposed of in any manner other than by
will or by the laws of descent or distribution and may be exercised, during the
lifetime of the Optionee, only by the Optionee.

    10.  Adjustments Upon Changes in Capitalization, Dissolution, Merger or
Asset Sale.  

    (a)  Changes in Capitalization.  Subject to any required action by the
stockholders of the Company, the number of Shares covered by each outstanding
Option, the number of Shares which have been authorized for issuance under the
Plan but as to which no Options have yet been granted or which have been
returned to the Plan upon cancellation or expiration of an Option, as well as
the price per Share covered by each such outstanding Option, and the number of
Shares issuable pursuant to the grant provisions of Section 4 hereof shall be
proportionately adjusted for any increase or decrease in the number of issued
Shares resulting from a stock split, reverse stock split, stock dividend,
combination or reclassification of the Common Stock, or any other increase or
decrease in the number of issued Shares effected without receipt of
consideration by the Company; provided, however, that conversion of any
convertible securities of the Company shall not be deemed to have been "effected
without receipt of consideration." Except as expressly provided herein, no
issuance by the Company of shares of stock of any class, or securities
convertible into shares of stock of any class, shall affect, and no adjustment
by reason thereof shall be made with respect to, the number or price of Shares
subject to an Option.

    (b)  Dissolution or Liquidation.  In the event of the proposed dissolution
or liquidation of the Company, to the extent that an Option has not been
previously exercised, it shall terminate immediately prior to the consummation
of such proposed action.

    (c)  Merger or Asset Sale.  In the event of a merger or consolidation of the
Company with or into another corporation or the sale of substantially all of the
assets of the Company, outstanding Options may be assumed or equivalent options
may be substituted by the successor corporation or a Parent or Subsidiary
thereof (the "Successor Corporation"). If an Option is assumed or substituted
for, the Option or equivalent option shall continue to be exercisable as
provided in Section 4 hereof for so long as the Optionee serves as a Director or
a director of the Successor Corporation. Following such assumption or
substitution, if the Optionee's status as a Director or director of the
Successor Corporation, as applicable, is terminated other than upon a voluntary
resignation by the Optionee, the Option or option shall become fully
exercisable, including as to Shares for which it would not otherwise be
exercisable. Thereafter, the Option or option shall remain exercisable in
accordance with Sections 8(b) through (d) above.

    If the Successor Corporation does not assume an outstanding Option or
substitute for it an equivalent option, the Option shall become fully vested and
exercisable, including as to Shares for which it would not otherwise be
exercisable. In such event the Board shall notify the Optionee that the Option
shall be fully exercisable for a period of thirty (30) days from the date of
such notice, and upon the expiration of such period the Option shall terminate.

    For purposes of this Section 10(c), an Option shall be considered assumed
if, following the merger, consolidation or sale of assets, the Option confers
the right to purchase or receive, for

5

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

each Share of Optioned Stock subject to the Option immediately prior to the
merger, consolidation or sale of assets, the consideration (whether stock, cash,
or other securities or property) received in the merger, consolidation or sale
of assets by holders of Common Stock for each Share held on the effective date
of the transaction (and if holders were offered a choice of consideration, the
type of consideration chosen by the holders of a majority of the outstanding
Shares). If such consideration received in the merger, consolidation or sale of
assets is not solely common stock of the successor corporation or its Parent,
the Administrator may, with the consent of the successor corporation, provide
for the consideration to be received upon the exercise of the Option, for each
Share of Optioned Stock subject to the Option, to be solely common stock of the
successor corporation or its Parent equal in fair market value to the per share
consideration received by holders of Common Stock in the merger, consolidation
or sale of assets.

    11.  Amendment and Termination of the Plan.  

    (a)  Amendment and Termination.  Except as set forth in Section 4, the Board
may at any time amend, alter, suspend, or discontinue the Plan, but no
amendment, alteration, suspension or discontinuation shall be made which would
impair the rights of any Optionee under any grant theretofore made, without his
or her consent. In addition, to the extent necessary and desirable to comply
with any applicable law or regulation, the Company shall obtain stockholder
approval of any Plan amendment in such manner and to such a degree as required.

    (b)  Effect of Amendment or Termination.  Any such amendment or termination
of the Plan shall not affect Options already granted and such Options shall
remain in full force and effect as if this Plan had not been amended or
terminated.

    12.  Time of Granting Options.  The date of grant of an Option shall, for
all purposes, be the date determined in accordance with Section 4 hereof.

    13.  Conditions Upon Issuance of Shares.  Shares shall not be issued
pursuant to the exercise of an Option unless the exercise of such Option and the
issuance and delivery of such Shares pursuant thereto shall comply with all
relevant provisions of law, including, without limitation, the Securities Act of
1933, as amended, the Exchange Act, the rules and regulations promulgated
thereunder, state securities laws, and the requirements of any stock exchange
upon which the Shares may then be listed, and shall be further subject to the
approval of counsel for the Company with respect to such compliance.

    As a condition to the exercise of an Option, the Company may require the
person exercising such Option to represent and warrant at the time of any such
exercise that the Shares are being purchased only for investment and without any
present intention to sell or distribute such Shares, if, in the opinion of
counsel for the Company, such representation is required by any of the
aforementioned relevant provisions of law.

    Inability of the Company to obtain authority from any regulatory body having
jurisdiction, which authority is deemed by the Company's counsel to be necessary
to the lawful issuance and sale of any Shares hereunder, shall relieve the
Company of any liability in respect of the failure to issue or sell such Shares
as to which such requisite authority shall not have been obtained.

    14.  Reservation of Shares.  The Company, during the term of this Plan, will
at all times reserve and keep available such number of Shares as shall be
sufficient to satisfy the requirements of the Plan.

    15.  Option Agreement.  Options shall be evidenced by written option
agreements in such form as the Board shall approve.

6

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

QuickLinks

ABGENIX, INC.
1998 DIRECTOR OPTION PLAN (As Amended and Restated Effective April 26, 2001)