<PAGE>

                                                                    Exhibit 10.3


                         REGISTRATION RIGHTS AGREEMENT


     This Registration Rights Agreement (this "Agreement") is entered into as of
                                               ---------
July 11, 2000, by and among Miller Exploration Company, a Delaware corporation
(the "Company"), and Guardian Energy Management Corp., a Michigan corporation
      -------
(the "Purchaser").
      --------


                                   RECITALS:
                                   --------

     A.   The Company and the Purchaser have entered into that certain
Securities Purchase Agreement of even date herewith (the "Purchase Agreement"),
                                                          ------------------
pursuant to which the Purchaser is acquiring a convertible promissory note (the
"Note") and certain warrants (the "Warrants") that are convertible into and
 ----                              --------
exercisable for shares (the "Shares") of the Company's common stock, par value
                             ------
$.01 per share ("Common Stock").
                 ------------

     B.   Pursuant to the terms of the Purchase Agreement, the Company has
agreed to register the shares of Common Stock received by the Purchaser pursuant
to the terms and conditions set forth herein.


                                  AGREEMENTS:
                                  ----------

     NOW, THEREFORE, for valuable consideration, the receipt and sufficiency of
which are hereby acknowledged, the parties hereto agree as follows:

     1.   Definitions.  As used herein, the following terms shall have the
          -----------
meanings indicated.

          "Commission" means the Securities and Exchange Commission.
           ----------

          "Exchange Act" means the Securities Exchange Act of 1934, as amended.
           ------------

          "Registrable Securities" means the shares of Common Stock received by
           ----------------------
the Purchaser pursuant to conversion of the Note and the exercise of the
Warrants and held of record by the Purchaser.  Any Registrable Security will
cease to be a Registrable Security when a registration statement under the
Securities Act covering such Registrable Security has been declared effective by
the Commission or when such Registrable Security is no longer held of record by
the Purchaser.

          "Securities Act" means the Securities Act of 1933, as amended.
           --------------

     2.   Shelf Registration Statement.  (a)  The Company will upon written
          ----------------------------
request from the Purchaser file a "shelf" registration statement on Form S-3
pursuant to Rule 415 under the Securities Act (the "Shelf Registration
                                                    ------------------
Statement"), with respect to the sale of the Registrable Securities.  The
Company shall use all commercially reasonable efforts to have the Shelf
Registration Statement
<PAGE>

declared effective by the Commission under the Securities Act as promptly as
practicable thereafter and to keep the Shelf Registration Statement effective
for a period of 180 days. The Company's obligations with respect to the Shelf
Registration Statement shall be subject to the limitations set forth below.

          (b) Notwithstanding the foregoing, if the Company shall furnish to the
Purchaser a certificate signed by the President of the Company stating that in
good faith judgment of the Board of Directors of the Company, it would be
seriously detrimental to the Company and its stockholders for a Shelf
Registration Statement to be filed and it is therefore essential to defer the
filing of such registration statement, the Company shall have the right to defer
such filing for a period of not more than 180 days after receipt of the request
of the Purchaser; provided, however, that the Company many not utilize this
                  --------  -------
right more than once in any twelve-month period.

          (c)  In addition and without limitation, the Company shall not be
obligated to effect, or to take any action to effect, any registration pursuant
to this Section 2;
        ---------

               (i)  After the Company has effected three registrations requested
     by the Purchaser pursuant to this Section 2 and such registrations have
                                       ---------
     been declared or ordered effective; or

               (ii) During the period starting with the date 60 days prior to
     the Company's good faith estimate of the date of filing of, and ending on a
     date 90 days after the effective date of, a registration subject to Section
                                                                         -------
     3 hereof; provided that the Company is actively employing in good faith all
     -
     commercially reasonable efforts to cause such registration statement to
     become effective.

          (d)  It shall be a condition precedent to the obligations of the
Company to take any action pursuant to this Section 2 with respect to the
                                            ---------
Registrable Securities of the Purchaser that the Purchaser furnish to the
Company such information regarding itself, the Registrable Securities held by
it, and the intended method of disposition of such securities as shall be
required to effect the registration of such Holder's Registrable Securities.

     3.   Piggyback Registration.
          ----------------------

          (a) Right to Piggyback.  If at any time the Company proposes to file a
              ------------------
registration statement under the Securities Act with respect to an offering of
Common Stock (except (i) on Form S-4, Form S-8 or any successor form thereto or
(ii) with respect to a distribution solely to existing stockholders of the
Company), whether or not for its own account, then the Company shall give
written notice of such proposed filing to the Purchaser at least 20 days before
the anticipated filing date (the "Piggyback Notice").  The Piggyback Notice
                                  ----------------
shall offer such holders the opportunity to register such amount of Registrable
Securities as the purchaser may request (a "Piggyback Registration").  Subject
                                            ----------------------
to Section 3(b) hereof, the Company shall include in each such Piggyback
   ------------
Registration all Registrable Securities requested to be included in the
registration for such offering. The Purchaser shall be permitted to withdraw all
or part of the Registrable Securities from a Piggyback Registration at any time
prior to the effective date of such Piggyback Registration.

                                      -2-
<PAGE>

          (b)  Priority on Piggyback Registrations.  The Company shall use
               -----------------------------------
commercially reasonable efforts to cause the managing underwriters of a proposed
underwritten offering of Common Stock to permit holders of Registrable
Securities requested to be included in the registration for such offering to
include all such Registrable Securities on the same terms and conditions as any
similar equity securities, if any, of the Company included therein.
Notwithstanding the foregoing, if the managing underwriters of such underwritten
offering determine in good faith that the total number of securities that such
holders, the Company, and any other persons having rights to participate in such
registration, propose to include in such offering is such as to materially and
adversely affect the success of such offering, then (x) if such Piggyback
Registration is a primary registration on behalf of the Company, the securities
to be offered (i) for the Purchaser and (ii) for the account of all other
persons other than the Company shall be reduced or limited pro rata in
                                                           --- ----
proportion to the respective dollar amounts of securities owned to the extent
necessary to reduce the total number of securities to be included in such
offering to the amount recommended by such managing underwriters, and (y) if
such Piggyback Registration is an underwritten secondary registration on behalf
of holders of equity securities of the Company, the Company shall include in
such registration:  (A) first, up to the full number of securities of such
persons exercising "demand" registration rights that in the opinion of such
underwriter can be sold (allocated among such holders as they may so determine),
and (B) second, the number of Registrable Securities included in such
registration pursuant to this Section 3 or "piggy-back" registration rights
                              ---------
contained in the other registration rights agreements in excess of the
securities such persons exercising "demand" registration rights propose to sell
that, in the opinion of such managing underwriter, can be sold without
materially and adversely affecting such offering (allocated pro rata on the
                                                            --- ----
basis of the aggregate dollar amount of securities owned).

     Notwithstanding the foregoing, to the extent that the priority provisions
set forth in this Section 3(b) are inconsistent with the priority provisions set
                  ------------
forth in any existing Registration Rights Agreements of the Company, then the
priority provisions contained in such Registration Rights Agreements will
control with respect to the shares of Common Stock requested to be included
pursuant to such Registration Rights Agreements. The provisions of this
paragraph shall not increase the number of Registrable Securities that a holder
could otherwise include pursuant to this Section 3 by reason of the allocation
                                         ---------
contained in the immediately preceding paragraph.

     4.   Registration Procedures.
          -----------------------

     The Company will as expeditiously as reasonably possible:

          (a)  furnish to the Purchaser, prior to filing the Shelf Registration
Statement, if requested in writing, copies of the Shelf Registration Statement
as proposed to be filed, and thereafter furnish to the Purchaser such number of
copies of the Shelf Registration Statement, each amendment and supplement
thereto (in each case including all exhibits thereto), the prospectus included
in the Shelf Registration Statement (including each preliminary prospectus) and
such other documents as the Purchaser may reasonably request in writing in order
to facilitate the disposition of the Registrable Securities owned by the
Purchaser;

                                      -3-
<PAGE>

          (b)  use all commercially reasonable efforts to register or qualify
the Registrable Securities under such other securities or blue sky laws of such
jurisdictions as the Purchaser may reasonably request and do any and all other
acts and things which may be reasonably necessary to enable the Purchaser to
consummate the disposition in such jurisdictions of the Registrable Securities;
provided that the Company will not be required to (i) qualify generally to do
--------
business in any jurisdiction where it would not otherwise be required to qualify
but for this subsection, (ii) subject itself to taxation in any such
jurisdiction or (iii) consent to general service of process in any such
jurisdiction;

          (c)  notify the Purchaser, at any time when a prospectus relating
thereto is required to be delivered under the Securities Act, of the occurrence
of an event requiring the preparation of a supplement or amendment to such
prospectus so that, as thereafter delivered to the purchasers of the Registrable
Securities, such prospectus will not contain an untrue statement of a material
fact or omit to state any material fact required to be stated therein or
necessary to make the statements therein not misleading and promptly make
available to the Purchaser any such supplement or amendment; and

          (d)  make available for inspection by the Purchaser and any attorney,
accountant or other professional retained thereby (collectively, the
"Inspectors"), all financial and other records, pertinent corporate documents
 ----------
and properties of the Company (collectively, the "Records") as shall be
                                                  -------
reasonably necessary to enable them to exercise their due diligence
responsibility, and cause the Company's officers, directors and employees to
supply all information reasonably requested by any such Inspectors in connection
with the Shelf Registration Statement.  Records which the Company determines, in
good faith, to be confidential and which it notifies the Inspectors are
confidential shall not be disclosed by the Inspectors unless (i) in the judgment
of counsel to the Company the disclosure of such Records is necessary to avoid
or correct a misstatement or omission in the Registration Statement or (ii) the
release of such Records is ordered pursuant to a subpoena or other order from a
court of competent jurisdiction.  The Purchaser agrees that information obtained
by it as a result of such inspections shall be deemed confidential and shall not
be used by it as the basis for any market transactions in the securities of the
Company unless and until such is made generally available to the public.  The
Purchaser further agrees that it will, upon learning that disclosure of such
Records is sought in a court of competent jurisdiction, give notice to the
Company and allow the Company, at its expense, to undertake appropriate action
to prevent disclosure of the Records deemed confidential.

     The Company may require the Purchaser to promptly furnish in writing to the
Company such information regarding the distribution of the Registrable
Securities as it may from time to time reasonably request and such other
information as may be legally required in connection with such registration.

     The Purchaser agrees that, upon receipt of any notice from the Company of
the happening of any event of the kind described in Section 4(c) hereof,
                                                    ------------
Purchaser will immediately discontinue disposition of Registrable Securities
pursuant to the Registration Statement until the Purchaser's receipt of the
copies of the supplemented or amended prospectus contemplated by Section 4(c)
                                                                 ------------
hereof, and, if so directed by the Company, the Purchaser will deliver to the
Company all copies,

                                      -4-
<PAGE>

other than permanent file copies then in the Purchaser's possession, of the most
recent prospectus covering such Registrable Securities at the time of receipt of
such notice. If the Company shall give such notice, the Company shall extend the
period during which the Registration Statement shall be maintained effective by
the number of days during the period from and including the date of the giving
of notice pursuant to Section 4(c) hereof to the date when the Company shall
make available to the Purchaser a prospectus supplemented or amended to conform
with the requirements of Section 4(c) hereof. The Purchaser acknowledges that
the delivery of any such notice shall constitute material non-public information
and agrees that it shall keep the existence of such notice confidential.

     5.   Registration Expenses.
          ---------------------

     In connection with the Registration Statement required to be filed
hereunder, the Company shall pay the following registration expenses:  (a) all
registration and filing fees; (b) the fees and expenses of the Company's
compliance with securities or blue sky laws (including reasonable fees and
disbursements of counsel in connection with blue sky qualifications of the
Registrable Securities); (c) printing expenses; (d) the reasonable fees and
disbursements of counsel for the Company and the customary fees and expenses for
independent certified public accountants retained by the Company; and (e) the
reasonable fees and expenses of any special experts retained by the Company in
connection with such registration.  The Company shall not have any obligation to
pay any legal fees of the Purchaser, any underwriting fees, discounts or
commissions attributable to the sale of Registrable Securities or any out-of-
pocket expenses of the Purchaser (or its agents).

     6.   Indemnification; Contribution.
          -----------------------------

          (a)  Indemnification by the Company.  The Company agrees to indemnify
               ------------------------------
and hold harmless the Purchaser from and against any and all losses, claims,
damages, liabilities and expenses (including reasonable costs of investigation)
arising out of or based upon any untrue statement or alleged untrue statement of
a material fact contained in the Registration Statement or prospectus contained
therein or in any amendment or supplement thereto or in any preliminary
prospectus, or arising out of or based upon any omission or alleged omission to
state therein a material fact required to be stated therein or necessary to make
the statements therein not misleading, except insofar as such losses, claims,
damages, liabilities or expenses arise out of, or are based upon, any such
untrue statement or omission or allegation thereof based upon information
furnished in writing to the Company by the Purchaser or on the Purchaser's
behalf expressly for use therein and; provided, further, that with respect to
                                      --------  -------
any untrue statement or omission or alleged untrue statement or omission made in
any preliminary prospectus, the indemnity agreement contained in this subsection
shall not apply to the extent that any such loss, claim, damage, liability or
expense results from the fact that a current copy of the prospectus was not sent
or given to the person asserting any such loss, claim, damage, liability or
expense at or prior to the written confirmation of the sale of the Registrable
Securities to such person if it is determined that it was the responsibility of
the Purchaser to provide such person with a current copy of the prospectus and
such current copy of the prospectus would have cured the defect giving rise to
such loss, claim, damage, liability or expense.

                                      -5-
<PAGE>

          (b)  Indemnification by Purchaser.  The Purchaser agrees to indemnify
               ----------------------------
and hold harmless, on a joint and several basis, the Company, its directors and
officers and each person, if any, who controls the Company within the meaning of
either Section 15 of the Securities Act or Section 20 of the Exchange Act to the
       ----------
same extent as the foregoing indemnity from the Company to the Purchaser, but
only with respect to information furnished in writing by the Purchaser or on the
Purchaser's behalf expressly for use in the Registration Statement or prospectus
relating to the Registrable Securities, any amendment or supplement thereto or
any preliminary prospectus.  In case any action or proceeding shall be brought
against the Company or its directors or officers, or any such controlling
person, in respect of which indemnity may be sought against the Purchaser, the
Purchaser shall have the rights and duties given to the Company, and the Company
or its directors or officers or such controlling person shall have the rights
and duties given to the Purchaser, by the preceding subsection hereof.

          (c)  Conduct of Indemnification Proceedings.  If any action or
               --------------------------------------
proceeding (including any governmental investigation) shall be brought or
asserted against any person entitled to indemnification under subsections (a) or
(b) above (an "Indemnified Party") in respect of which indemnity may be sought
               -----------------
from any party who has agreed to provide such indemnification (an "Indemnifying
                                                                   ------------
Party"), the Indemnifying Party shall assume the defense thereof, including the
-----
employment of counsel reasonably satisfactory to such Indemnified Party, and
shall assume the payment of all expenses.  Such Indemnified Party shall have the
right to employ separate counsel in any such action and to participate in the
defense thereof, but the fees and expenses of such counsel shall be at the
expense of such Indemnified Party unless (i) the Indemnifying Party has agreed
to pay such fees and expenses or (ii) the named parties to any such action or
proceeding (including any impleaded parties) include both such Indemnified Party
and the Indemnifying Party, and such Indemnified Party shall have been advised
by counsel that there is a conflict of interest on the part of counsel employed
by the Indemnifying Party to represent such Indemnified Party (in which case, if
such Indemnified Party notifies the Indemnifying Party in writing that it elects
to employ separate counsel at the expense of the Indemnifying Party, the
Indemnifying Party shall not have the right to assume the defense of such action
or proceeding on behalf of such Indemnified Party; it being understood, however,
that the Indemnifying Party shall not, in connection with any one such action or
proceeding or separate but substantially similar or related actions or
proceedings in the same jurisdiction arising out of the same general allegations
or circumstances, be liable for the fees and expenses of more than one separate
firm of attorneys (together with appropriate local counsel) at any time for all
such Indemnified Parties, which firm shall be designated in writing by such
Indemnified Parties).  The Indemnifying Party shall not be liable for any
settlement of any such action or proceeding effected without its written
consent, but if settled with its written consent, or if there be a final
judgment for the plaintiff in any such action or proceeding, the Indemnifying
Party shall indemnify and hold harmless such Indemnified Parties from and
against any loss or liability (to the extent stated above) by reason of such
settlement or judgment.

          (d)  Contribution.  If the indemnification provided for in this
               ------------
Section 6 is unavailable to the Indemnified Parties in respect of any losses,
---------
claims, damages, liabilities or judgments referred to herein, then each
Indemnifying Party, in lieu of indemnifying such Indemnified Party, shall
contribute to the amount paid or payable by such Indemnified Party as a result
of such losses, claims, damages, liabilities and judgments in the following
manner: as between

                                      -6-
<PAGE>

the Company on the one hand and each Shareholder on the other, in such
proportion as is appropriate to reflect the relative fault of the Company on the
one hand and each Shareholder on the other in connection with the statements or
omissions which resulted in such losses, claims, damages, liabilities or
judgments, as well as any other relevant equitable considerations.  The relative
fault of the Company on the one hand and of the Purchaser on the other shall be
determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or the omission or alleged omission to state
a material fact relates to information supplied by such party, and the party's
relative intent, knowledge, access to information and opportunity to correct or
prevent such statement or omission.  No person guilty of fraudulent
misrepresentation (within the meaning of subsection 11(f) of the Securities Act)
shall be entitled to contribution from any person who was not guilty of such
fraudulent misrepresentation.

          (e)  Survival.  The indemnity and contribution agreements contained in
               --------
this Section 6 shall remain operative and in full force and effect regardless of
     ---------
(i) any termination of this Agreement, (ii) any investigation made by or on
behalf of any Indemnified Party or by or on behalf of the Company and (iii) the
consummation of the sale or successive resale of the Registrable Securities.

     7.   Miscellaneous.
          -------------

          (a)  Amendments and Waivers.  The provisions of this Agreement may not
               ----------------------
be amended, modified or supplemented, and waivers or consents to departures from
the provisions hereof may not be given other than as initially agreed upon in
writing by the Company and the Purchaser.

          (b)  Notices.  All notices and other communications hereunder shall be
               -------
in writing and shall be deemed given upon (i) transmitter's confirmation of a
receipt of a facsimile transmission, (ii) confirmed delivery by a standard
overnight carrier or when delivered by hand or (iii) the expiration of two
business days after the day when mailed, postage prepaid, addressed at the
following addresses (or at such other address for a party as shall be specified
by like notice):

               (iv)  if to the Purchaser, at the most current address given by
     the Purchaser to the Company, in accordance with the provisions of this
     subsection, which address initially is Guardian Energy Management Corp.,
     2300 Harmon Road, Auburn Hills, Michigan 48326-1714, Attention Vice
     President - Operations, Facsimile No. 248-340-2258, with copy to its
     Secretary, Facsimile No.: 248-340-2175, and thereafter to such other
     address as may be designated from time to time by notice given in
     accordance with the provisions of this Section.

               (v)   if to the Company, initially at 3104 Logan Valley Road,
     Traverse City, Michigan 49685, Attention: Chief Executive Officer,
     Facsimile No.: (231) 941-8312, with a copy of Vinson & Elkins L.L.P., 2001
     Ross Avenue, Suite 3700, Dallas, Texas 75201, Facsimile No.: (214)
     999-7985, Attention: Mark Early, and thereafter at such other address as
     may be designated from time to time by notice given in accordance with the
     provisions of this Section.

                                      -7-
<PAGE>

          (c)  Successors and Assigns.  The Purchaser shall not assign any
               ----------------------
rights or benefits under this Agreement without the prior written consent of the
Company; provided, however, that the Purchaser may assign to any Permitted
Assignee (as that term is defined in the Securities Purchase Agreement) such
rights or benefits without the consent of the Company with respect to Securities
or Conversion Shares transferred to such Permitted Assignee. This Agreement
shall inure to the benefit of and be binding upon the permitted successors and
assigns of the Company and the Purchaser.

          (d)  Counterparts.  This Agreement may be executed in a number of
               ------------
identical counterparts and it shall not be necessary for the Company and the
Purchaser to execute each of such counterparts, but when each has executed and
delivered one or more of such counterparts, the several parts, when taken
together, shall be deemed to constitute one and the same instrument, enforceable
against each in accordance with its terms.  In making proof of this Agreement,
it shall not be necessary to produce or account for more than one such
counterpart executed by the party against whom enforcement of this Agreement is
sought.

          (e)  Headings.  The headings in this Agreement are for convenience of
               --------
reference only and shall not limit or otherwise affect the meaning hereof.

          (f)  Governing Law.  THIS AGREEMENT SHALL BE GOVERNED BY AND CONSTRUED
               -------------
IN ACCORDANCE WITH THE LAWS OF THE STATE OF DELAWARE, WITHOUT REGARD TO
PRINCIPLES OF CONFLICTS OR CHOICE OF LAW.

          (g)  Severability.  If any provision of this Agreement is held to be
               ------------
illegal, invalid or unenforceable under present or future laws effective during
the term of this Agreement, such provision shall be fully severable; this
Agreement shall be construed and enforced as if such illegal, invalid or
unenforceable provision had never comprised a part of this Agreement; and the
remaining provisions of this Agreement shall remain in full force and effect and
shall not be affected by the illegal, invalid or unenforceable provision or by
its severance from this Agreement.  Furthermore, in lieu of each such illegal,
invalid or unenforceable provision, there shall be added automatically as a part
of this Agreement a provision as similar in terms to such illegal, invalid or
unenforceable provision as may be possible and be legal, valid and enforceable.

          (h)  Entire Agreement.  This Agreement is intended by the Company and
               ----------------
the Purchaser as a final expression of their agreement and is intended to be a
complete and exclusive statement of their agreement and understanding in respect
of the subject matter contained herein. This Agreement supersedes all prior
agreements and understandings between the Company and the Purchaser with respect
to such subject matter.

          (i)  Third Party Beneficiaries.  Other than Indemnified Parties not a
               -------------------------
party hereto, this Agreement is intended for the benefit of the Company and the
Purchaser and their respective successors and permitted assigns and is not for
the benefit of, nor may any provision hereof be enforced by, any other person or
entity other than Permitted Assignees with respect to Securities or Conversion
Shares that the Purchaser has transferred to such Permitted Assignees.

                                      -8-
<PAGE>

     IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of
the date first above written.

                              MILLER EXPLORATION COMPANY



                              By: /s/ Kelly E. Miller
                                 ----------------------------------------------
                              Name: Kelly E. Miller
                                   ---------------------------------------------
                              Title: President
                                    --------------------------------------------



                              GUARDIAN ENERGY MANAGEMENT CORP.



                              By: /s/ Paul A. Halpern
                                 -----------------------------------------------
                              Name: Paul A. Halpern
                                   ---------------------------------------------
                              Title: Vice President - Operations
                                    --------------------------------------------

                                      -9-