<PAGE>   1
                                                                    EXHIBIT 10.3

                              CONSULTING AGREEMENT


         This CONSULTING AGREEMENT (this "Agreement") is entered into as of the
effective date specified below by and between ARONEX PHARMACEUTICALS, INC., a
Delaware corporation (the "Company"), and the undersigned consultant whose name
and address appear below ("Consultant"). The Company and Consultant hereby agree
as follows:

         1. CONSULTING SERVICES. Consultant is hereby engaged by the Company as
an independent contractor, and not as an employee, to carry out the project
specified in the Description of Work attached hereto as Exhibit A, on the terms
and conditions set forth in such Description of Work.

         2. TERM. This Agreement shall commence on October 1, 1999 and shall
automatically renew for successive one year periods. This Agreement may be
terminated by Consultant or Company, with or without "cause" (as defined below),
by giving 30 days' advance written notice thereof to the other party hereto. In
addition, this Agreement may be terminated by the Company immediately for
"cause." For purposes of this Agreement, "cause" shall be deemed to exist for
termination of this Agreement by the Company in the event (i) Consultant is not
performing in compliance with the Description of Work, (ii) Consultant has
engaged in personal conduct which (in the good faith determination of the
Company) would materially injure the goodwill or reputation of the Company or
otherwise materially adversely affect the interests of the Company or (iii) of
any breach by Consultant of the obligations contained in this Agreement or any
other agreement between the Company and Consultant.

         In the event of any termination of this Agreement prior to completion
of the term of this Agreement pursuant to the above provisions (whether with or
without "cause"), the Company's sole liability thereupon will be to pay
Consultant any unpaid balance due for work performed up to and including the
date of termination, if applicable.

         3. INDEPENDENT CONTRACTOR. It is agreed that Consultant's services are
made available to the Company on the basis that Consultant will retain
Consultant's individual professional status and that Consultant's relationship
with the Company is that of an independent contractor and not that of an
employee. Consultant will not be eligible for any employee benefits, nor will
the Company make deductions from its fees to Consultant for taxes, insurance,
bonds or any other subscription of any kind. Consultant will use Consultant's
own discretion in performing the tasks assigned, within the scope of work
specified by the Company. Consultant agrees to indemnify and hold the Company
harmless from and against any claim made by any third party against the Company
based in whole or in part upon any action by Consultant or any of Consultant's
employees, associates, consultants, agents, representatives, assignees or
successors in interest (collectively, "Consultant's Associates"), which occurs
pursuant to or in connection with this Agreement or the relationship or
relationships contemplated by this Agreement.

         4. CONFIDENTIAL INFORMATION. Consultant agrees that Consultant, and all
of Consultant's Associates, shall keep in strictest confidence all information
relating to the products, materials, programs, algorithms, designs, trade
secrets, secret processes, customers and markets of the Company and all other
confidential knowledge, data and information related to the business or affairs
of the Company (collectively, "Confidential Information") that may be acquired
pursuant to or in connection with this Agreement or the relationship or
relationships contemplated by this Agreement. During and after the term of this
Agreement, neither Consultant nor any of Consultant's Associates will, without
the prior written consent of an officer of the Company, publish, communicate,
disclose or use for any purpose any of such Confidential Information. Upon
termination of this Agreement, Consultant will return to the Company all
records, data, notes, reports, printouts, sketches, material, equipment and
other documents or property, and all


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reproductions of any of the foregoing, furnished by the Company or developed or
prepared pursuant to the relationship hereunder.

         Notwithstanding the foregoing, it is agreed that Confidential
Information shall not include any (i) information which is or becomes through no
fault of Consultant or any of Consultant's Associates generally known to the
public, and (ii) Consultant's and Consultant's Associates' skill, knowledge,
know-how and experience.

         5. ASSIGNMENT OF INTELLECTUAL PROPERTY. Consultant agrees to transfer
and assign and hereby does transfer and assign to the Company the entire right,
title and interest for the entire world in and to all data, materials, software,
designs, models, algorithms, writings, drawings, notebooks, documents,
photographs, inventions and discoveries (collectively, "Inventions") made or
conceived or reduced to practice by Consultant or any of Consultant's Associates
(i) in the course of accomplishing the work described on the Description of Work
attached as Exhibit A hereto, (ii) in the course of accomplishing other work
performed pursuant to the relationship established by this Agreement, or (iii)
with the use of materials or facilities of the Company.

         Consultant agrees that Consultant and each of Consultant's Associates
will sign, execute and acknowledge, or cause to be signed, executed and
acknowledged, at the expense of the Company, any and all documents, and will
perform any and all acts, as may be necessary, useful or convenient for the
purpose of securing to the Company or its nominee patent, trademark or copyright
protection throughout the world upon all such Inventions. At the request of the
Company, Consultant will have each of Consultant's Associates with access to
Confidential Information of the Company or who performs work pursuant to this
Agreement to sign an agreement in form substantially identical to this
Agreement.

         6. LICENSE RIGHTS. In the event that Consultant recommends to the
Company that the Company make use of devices and/or processes covered by patents
and/or patent applications which Consultant may own or control, Consultant will
then so inform the Company, and in the event that the Company shall follow
Consultant's recommendation and Consultant has the right to grant a license
under such patents and/or patent applications, then Consultant will grant to the
Company a license on reasonable terms which are no less favorable than those
granted by Consultant to any other licensee.

         7. REPRESENTATIONS OF CONSULTANT AND THE COMPANY.

                  1. Consultant represents and warrants to the Company that (i)
this Agreement is a valid and binding obligation of Consultant, enforceable
against Consultant in accordance with its terms, and (ii) his execution and
delivery of, and performance of his services and other obligations under, this
Agreement will not result in the breach or violation of applicable law or any
agreement to which he is a party.

                  2. The Company represents and warrants to Consultant that (i)
this Agreement has been duly and validly authorized by the Company and is a
valid and binding obligation of the Company, enforceable against the Company in
accordance with its terms, and (ii) its execution and delivery of, and
performance of its obligations under, this Agreement will not result in the
breach or violation of applicable law or any agreement to which it is a party.


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         8.       MISCELLANEOUS.

                  1. Effective Date. This Agreement shall be effective as of the
effective date specified below, and it is expressly agreed to by Consultant and
the Company that all the provisions hereof shall apply as if this Agreement had
been entered into on such date.

                  2. Survival of Terms. The provisions of paragraphs 4, 5 and 6
hereof shall survive termination of this Agreement.

                  3. Successors and Assigns. This Agreement may not be assigned
by Consultant without the written consent of the Company. This Agreement shall
be binding on all of Consultant's Associates, all of Consultant's heirs,
executors, administrators and legal representatives, and all of Consultant's
successors in interest and assigns, and shall be for the benefit of the Company,
its successors and its assigns.

                  4. Governing Law. This Agreement shall be governed by and
construed and enforced in accordance with the laws of the State of Texas as they
apply to contracts entered into and wholly to be performed in Texas.

                  5. Severability. If one or more of the provisions in this
Agreement are deemed void by law, then the remaining provisions will continue in
full force and effect.

                  6. Amendment. Neither this Agreement nor the Description of
Work may be amended except by a written agreement modifying the appropriate
document duly executed by Consultant and an officer of the Company.

                  7. Entire Agreement. This Agreement, together with the
Description of Work attached hereto and any other confidentiality agreement
previously or subsequently entered into by the Company and Consultant,
constitutes the sole and complete agreement of the parties with respect to the
matters included herein, and supersedes any previous oral or written agreement,
if any, relating to the subject matters included herein.

                  8. No Conflict. Consultant represents and warrants that this
Agreement does not conflict with any other agreement or term of employment
applicable to or binding upon the Consultant as of the date hereof and that
Consultant will promptly notify the Company in the event that any such conflict
does arise during the term hereof.

                  9. Construction. Each party to this Agreement has had the
opportunity to review this Agreement with legal counsel. This Agreement shall
not be construed or interpreted against any party on the basis that such party
drafted or authored a particular provision, parts of or the entirety of this
Agreement.



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         IN WITNESS WHEREOF, this Agreement has been executed on the date set
forth below, and shall be effective as of the date specified.

CONSULTANT:                               COMPANY:

DAVID J. MCLACHLAN                        ARONEX PHARMACEUTICALS, INC.


By:   /s/ DAVID J. MCLACHLAN              By:    /s/ GEOFFREY F. COX, PH.D.
   ---------------------------------         --------------------------------
Name: David J. McLachlan                  Name:  Geoffrey F. Cox, Ph.D.
     -------------------------------           ------------------------------
                                          Title: CEO
                                                -----------------------------
Date: September 30, 1999                  Date:  September 28, 1999
     -------------------------------           ------------------------------

Effective Date: October 1, 1999






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<PAGE>   5
                                    EXHIBIT A

                          ARONEX PHARMACEUTICALS, INC.

                               DESCRIPTION OF WORK

                  (CONSULTING AGREEMENT DATED OCTOBER 1, 1999)


1.       DETAILED DESCRIPTION OF WORK:

         Consultant will perform work under this Agreement regarding accounting
and financial matters, as may be mutually agreed, from time to time, between the
Company and Consultant. Consultant will provide at least 20 days of consulting
services per year. The specific terms of such projects, including the detailed
description of the work to be performed and the completion date of any project,
if any, shall be required to be set forth in writing, in which case such terms
shall constitute an addendum to this Agreement.

2.       START DATE: October 1, 1999

         COMPLETION DATE: Automatically renew upon anniversary date for
successive one year terms unless 30 days' advance written notice is given.

3.       PERSON(S) WHO ARE TO PERFORM THE WORK:

         David J. McLachlan

4.       AUTHORIZED REPRESENTATIVE OF THE COMPANY:

         The character of Consultant's services shall be subject to the
assignment and direction of Geoffrey Cox, Ph.D., who will be designated as the
"Director." Further, the character and scope of Consultant's services may be
revised by mutual agreement between Consultant and the Company and such revision
will be evidenced by a formal bilateral modification to the Consulting Agreement
or this Description of Work signed between Consultant and an authorized officer
of the Company. The Director and the Chief Executive Officer of the Company
shall be the only individuals authorized to designate any project to be covered
by this Agreement, sign any modification or addendum to this Agreement or the
Description of Work, and direct the activities of Consultant under this
Agreement.

5.       SCHEDULE PERFORMANCE:

         If at any time during the performance of this contract any phase of the
required tasks appear to be impossible of execution or if any phase cannot be
completed on schedule, it is agreed that Consultant will notify the Company
within one (1) day of such determination. At the time of such notification
Consultant shall explain to the Company why a particular task is impossible to
complete and propose alternative procedures for achieving the desired result.

6.       REPORT SCHEDULE:

         Reports, if any, to be as specified in an addendum to this Agreement.

7.       PAYMENT:


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         As consideration for all services to be rendered and performed under
this Agreement and for assigning the rights to inventions, designs, patents,
trademarks, and copyrights as provided in the Consulting Agreement, Consultant
will be paid a consulting fee of $2,500.00 per month, 50% payable in Aronex
Pharmaceuticals, Inc. common stock and 50% in cash. The cash will be paid on a
monthly basis and the stock will be issued quarterly. The number of shares of
Common Stock to be granted shall be determined by reference to the fair market
value of the Common Stock as of the first day of each month.

8.       EXPENSES:

         The Company agrees to reimburse Consultant for the following expenses
incurred in connection with the performance of Consultant's services under this
Agreement:


<TABLE>
<CAPTION>
                                                                 Yes       No
                                                                 ---       --
<S>                <C>                                           <C>       <C>
          -        Routine out-of-pocket expense                  X
          -        Local travel                                   X
          -        Long distance travel at the direction          X
                   of the Director or President
          -        Other - as approved in advance                 X
</TABLE>

CONSULTANT:                            COMPANY:

DAVID J. MCLACHLAN                     ARONEX PHARMACEUTICALS, INC.


By: /s/ David J. McLachlan             By: /s/ Geoffrey F. Cox
   -------------------------              ------------------------------
Name: David J. McLachlan               Name:  Geoffrey F. Cox, Ph.D.
     -----------------------                ----------------------------
                                       Title:   CEO
                                             ---------------------------
Date: September 30, 1999               Date: September 28, 1999
     -----------------------                ----------------------------


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