As filed with the Securities and Exchange Commission on July 20, 2004

Registration No. 333-114460

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549

_________________

AMENDMENT NO. 2TOFORM S-3
REGISTRATION STATEMENT
Under The Securities Act of 1933

_________________

ORPHAN MEDICAL, INC.(Exact name of registrant as specified in its charter)

|Delaware
(State or other jurisdiction of incorporation or
organization) | 41-1784594
(I.R.S. Employer Identification No.)
|----------------------------------------------------------------------- | -----------------------------------------------

John Howell Bullion
Chief Executive Officer
Orphan Medical, Inc.
13911 Ridgedale Drive
Suite 250
Minnetonka, MN 55405
(952) 513-6900

Copies to:
Philip E. Bauer, Esq.
Dorsey & Whitney LLP
50 South Sixth Street, Suite 1500
Minneapolis, Minnesota 55402
(Name, address, including zip code, and telephone number, including area code, of agent for service)

_________________

Approximate
date of commencement of proposed sale to the public: As soon as practicable
after the Registration Statement becomes effective.

If
the only securities being registered on this Form are being offered pursuant to
dividend or interest reinvestment plans, please check the following
box. o

If
any of the securities being registered on this Form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box.
x

If
this Form is filed to register additional securities for an offering pursuant to
Rule 462(b) under the Securities Act, please check the following box and
list the Securities Act registration statement number of the earlier effective
registration statement for the same offering.o

If
this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities
Act, check the following box and list the Securities Act registration statement number of
the earlier effective registration statement for the same offering.o

If
delivery of the prospectus is expected to be made pursuant to Rule 434, please check the
following box. o

The
Registrant hereby amends this Registration Statement on such date or dates as may be
necessary to delay its effective date until the Registrant shall file a further amendment
which specifically states that this Registration Statement shall thereafter become
effective in accordance with Section 8(a) of the Securities Act of 1933 or until the
Registration Statement shall become effective on such date as the Commission, acting
pursuant to said Section 8(a), may determine.

---

The information in this
prospectus is not complete and may be changed. We may not sell these securities
until the registration statement filed with the Securities and Exchange
Commission is effective. This prospectus is not an offer to sell these
securities and it is not soliciting an offer to buy these securities in any
jurisdiction where the offer or sale is not permitted.

|PRELIMINARY PROSPECTUS | Subject to Completion, dated July 20, 2004
|---------------------- | ------------------------------------------

_________________

# ORPHAN MEDICAL, INC.

# 4,000,000 Common Shares

_________________

We
may from time to time sell up to 4,000,000 shares of our common stock through public or
private transactions, on or off the Nasdaq National Market, at prevailing market prices or
at privately negotiated prices.

This
prospectus describes the general manner in which our common stock may be offered using
this prospectus. We will provide the specific terms of the offering in supplements to this
prospectus. This prospectus may not be used to offer and sell our common stock unless
accompanied by a prospectus supplement.

Our
common stock is traded on the Nasdaq National Market under the symbol ORPH. On
July 9, 2004, the last sale price of our common stock as reported on the Nasdaq National
Market was $8.79 per share.

_________________

Neither
the Securities and Exchange Commission nor any state securities commission has approved or
disapproved of these securities or determined if this prospectus is truthful or complete.
Any representation to the contrary is a criminal offense.

The
shares of common stock we offer may involve a high degree of risk. The risks
associated with an investment in our shares are described beginning on page 27
of our Form 10-K/A (Amendment No. 3) filed with the Securities and Exchange Commission on July 20, 2004.

_________________

# The date of this
prospectus is           , 2004.



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# TABLE OF CONTENTS

|                                                          | PAGE
|--------------------------------------------------------- | ----
|Prospectus Summary                                        | 3   
|Orphan Medical, Inc.                                      | 4   
|Cautionary Statement Regarding Forward-Looking Statements | 5   
|Use of Proceeds                                           | 6   
|Description of Capital Stock                              | 7   
|Plan of Distribution                                      | 11  
|Legal Matters                                             | 12  
|Experts                                                   | 12  
|Where You Can Find More Information                       | 12  

-2-

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# PROSPECTUS SUMMARY

This
prospectus is part of a registration statement that we filed with the SEC using
a shelf registration process. Under this shelf process, each time we
sell shares of our common stock using this prospectus, we will provide a
prospectus supplement that will contain specific information about the terms of
that offering and may supplement information contained in this prospectus. You
should read this prospectus and the applicable prospectus supplement together
with the additional information described under the heading Where You Can
Find More Information.

You
should rely only on the information contained or incorporated by reference in this
prospectus. We have not authorized any other person to provide you with different
information. If anyone provides you with different or inconsistent information, you should
not rely on it. We are not making an offer to sell these securities in any jurisdiction
where the offer or sale is not permitted. You should assume that the information appearing
in this prospectus is accurate only as of the date on the front cover of this prospectus,
even if this prospectus is delivered to you after that date or you buy shares of our
common stock after that date. Our business, financial condition, results of operations and
prospects may have changed since that date. Information contained on our website does not
constitute part of this prospectus. In this prospectus, references to Orphan,
we, us and our refer to Orphan Medical, Inc.

The
registration statement that contains this prospectus (including the exhibits filed with
and incorporated by reference to the registration statement) contains additional
information about us and the shares of our common stock offered under this prospectus.
That registration statement can be read at the SEC web site or at the SEC offices
mentioned under the heading Where You Can Find More Information.

-3-

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# ORPHAN MEDICAL, INC.

Orphan
Medical, Inc. is a specialty pharmaceutical company focused primarily on sleep
disorders, pain and other central nervous system (CNS) disorders. We seek to
acquire, develop and market pharmaceutical products that are prescribed by
physician specialists and offer a major improvement in the safety or efficacy of
patient treatment and have no substantially equivalent substitute.

The Companys lead product, Xyrem® (sodium oxybate) solution is approved for the treatment of cataplexy, a
debilitating symptom of narcolepsy, a sleep disorder.   The Company markets Xyrem using a 37 person specialty
sales force that focuses its selling efforts on physicians specializing in the treatment of sleep disorders.
Clinical trials conducted in accordance with United States Food and Drug Administration (FDA) approved protocols
have shown that Xyrem consolidates sleep and increases sleep continuity and non-REM sleep, particularly Stages
III and IV, which stages are known as slow-wave sleep.  Stages III and IV are the stages in which the body
experiences the greatest level of restoration. Although currently available hypnotics facilitate sleep onset and
maintenance, they tend to reduce rather than increase slow-wave sleep. The active ingredient of Xyrem, sodium
oxybate or gamma hydroxybutyrate, has also been shown to have other activity that may have therapeutic
significance.

Recognizing
the significant long-term potential of Xyrem, the Company has initiated a range
of clinical development and product development programs. The Company has
initiated two Phase III(b) clinical trials to assess the efficacy of Xyrem
in the treatment of excessive daytime sleepiness (EDS) and other symptoms of
narcolepsy. The first trial is complete and the data was announced on
May 19, 2004. The data showed that Xyrem, at certain doses, provides
statistically significant improvement in specific measurements of EDS associated
with narcolepsy. The second trial is expected to be completed late in the third
quarter of 2004. If the results of these trials are positive, Xyrem could be
marketed to the entire narcolepsy market, which is estimated to affect
approximately .05% of the population or 100,000 to 140,000 persons in the United
States. We also expect to begin a clinical trial in the first half of 2004 to
assess Xyrem in treating the symptoms of Fibromyalgia Syndrome (FMS). FMS is a
chronic condition characterized by widespread muscular pain, musculoskeletal
discomfort, fatigue, and systemic symptoms. FMS is estimated to affect over 4
million Americans. If Xyrem demonstrates efficacy in treating certain FMS
symptoms, additional trials will be conducted in order to obtain FDA approval to
market Xyrem to physicians treating this condition. We are also assessing
development of an unrelated product, Butamben (butyl-p-amino benzoate), for the
treatment of cancer pain.

In
addition to expanding the labeling of Xyrem and developing Butamben, we plan to
build our presence in specialty CNS markets through the acquisition of both
development stage compounds and marketed products. The Company generally seeks
to develop products that (1) have some clinical history, (2) have a
straightforward formulation that can be readily manufactured with established
technologies, and (3) do not require excessive specialized processes for
development or manufacture. We do not conduct extensive basic research to
discover new chemical entities. Instead, we generally seek to acquire products
that are already in clinical trials. Medicines developed or acquired in the
future may hold orphan drug status, although we may develop or acquire products
that do not hold such status if we can obtain appropriate proprietary protection
through patents or otherwise. A drug that has orphan drug designation and which
is the first product to receive marketing approval for its product claim,
indication or application, receives orphan drug status and is entitled to a
seven-year exclusive marketing period in the United States for that product
claim and a 10-year exclusive period in Europe for that product claim,
indication or application, subject to certain limitations.

Since
its inception, the Company has obtained New Drug Application (NDA) approvals
from the United States Food and Drug Administration (FDA) for six specialty
pharmaceutical products. Each of the NDAs was granted Orphan Drug Status by the
FDA. In the second quarter of 2003, we sold all rights to three of these
products in order to concentrate resources on Xyrem and enhance our focus on
sleep, pain and specialty CNS markets. We currently market the three remaining
NDA approved drugs: Xyrem® (sodium oxybate) oral solution, for the treatment
of cataplexy associated with narcolepsy; Antizol® (fomepizole) Injection, an
antidote for ethylene glycol or suspected ethylene glycol ingestion in humans
and an antidote for methanol or suspected methanol ingestion in humans; and
Cystadane® (betaine anhydrous for oral solution), for homocystinuria, a
genetic disease. We also market a fourth product, Antizol-Vet® (fomepizole)
for injection, which is an antidote for ethylene glycol or suspected ethylene
glycol ingestion in dogs. This product was approved using a New Animal Drug
Application (NADA).

Our
activities have consisted primarily of obtaining the rights for pharmaceutical products,
hiring the personnel required to implement our business plan, managing the development of
these products, preparing for the commercial introduction of these products and raising
capital to support our business operations.

Orphan Medical, Inc. was incorporated on June 17, 1994 as a Minnesota corporation to carry on the
business previously conducted by the Orphan Medical division of Chronimed, Inc. The business was reincorporated
as a Delaware corporation on September 1, 2000. We have not generated sufficient levels of revenue from our
approved products to date to fund our operating activities and have sustained significant operating losses each
year since inception. We expect operating losses to continue at least through 2004. Our operations to date have
not been profitable and, as of March 31, 2004, we have an accumulated deficit of $60.8 million since inception.

-4-

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# CAUTIONARY STATEMENT
REGARDING FORWARD-LOOKING STATEMENTS

Certain statements contained in this prospectus constitute forward-looking statements within the
meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and are subject
to the safe harbor created by that statute. In some cases, you can identify forward
looking statements by terminology such as expects, anticipates,
intends, may, should, plans,
believes, seeks, estimates, could,
would or the negative of such terms or other comparable terminology. Such
forward-looking statements are based upon current expectations and beliefs and involve
numerous risks and uncertainties, both known and unknown, that could cause actual events
or results to differ materially from these forward-looking statements. Although we believe
that the expectations reflected in the forward-looking statements are reasonable as of the
date of this prospectus, we cannot guarantee future results, levels of activity,
performance or achievements. We undertake no duty to update any of the forward-looking
statements after the date of this prospectus.

-5-

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# USE OF PROCEEDS

Except as otherwise provided in the applicable prospectus supplement, we will use the net proceeds from the sale
of common stock hereunder to fund clinical trial activities, for certain sales and marketing activities and for
general corporate purposes.

Although we believe we have sufficient cash available for currently anticipated clinical trials, proceeds
might be used for trials related to products that we may acquire or develop in the future or for trials related
to new indications of existing products.

We may also use a portion of the proceeds to fund product acquisition, although we currently have no specific new
product acquisition or development plans.

-6-

---

# DESCRIPTION OF CAPITAL STOCK

The
total number of shares of authorized capital stock of the Company is 25,000,000, of which
14,000 shares are designated Senior Convertible Preferred Stock, $.01 par value, 5,000
shares are designated Series B Convertible Preferred Stock, $.01 par value, 4,000 shares
are designated Series C Convertible Preferred Stock, $.01 par value, 1,500,000 shares are
designated Series D Non-Voting Preferred Stock, $.01 par value, and the remaining
23,477,000 shares are deemed common stock unless specifically designated otherwise by our
board of directors.

Common Stock

As
of June 30, 2004, there were 10,900,549 shares of Orphan Medical, Inc. common stock
outstanding. The Orphan Medical common stock is listed on the Nasdaq National Market under
the symbol ORPH.

Voting and Other Rights

Each
share of Orphan Medical common stock is entitled to one vote per share, and, in general, a
majority of votes cast with respect to a matter will be sufficient to authorize action
upon routine matters. Directors are to be elected by a majority of the votes cast, and
shareholders do not have the right to cumulate their votes in the election of directors.
For that reason, holders of a majority of the shares of common stock of Orphan Medical
entitled to vote in any election of directors may elect all of the directors standing for
election. In general, however:

| |  | amendments
to the certificate of incorporation will be approved if the votes cast within a voting
group favoring the action exceed the votes cast within the voting group opposing the
action; and
|- |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| |  | a
merger or dissolution of Orphan Medical, or the sale of all or substantially all
of its assets, must be approved by the affirmative vote of the holders of a
majority of the voting power of the outstanding voting shares and the
affirmative vote of the holders of a majority of the outstanding shares of each
class entitled to vote on the matter as a class.
|- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

No Preemptive or Conversion Rights

Orphan
Medical common stock will not entitle its holders to any preemptive rights, redemption
privileges, sinking fund privileges or conversion rights.

Assets upon Dissolution

In
the event of liquidation, holders of Orphan Medical common stock would be entitled to
receive proportionately any assets legally available for distribution to Orphan Medical
shareholders with respect to shares held by them, subject to any prior rights of any
preferred stock of Orphan Medical then outstanding.

-7-

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Distributions

Holders
of Orphan Medical common stock will be entitled to receive the dividends or distributions
that Orphan Medicals board of directors may declare out of funds legally available
for these payments. The payment of distributions by Orphan Medical is subject to the
restrictions of Delaware law applicable to the declaration of distributions by a
corporation. Under Delaware law, a corporation may not pay a dividend out of net profits
if the capital stock of the corporation is less than the stated amount of capital
represented by the issued and outstanding stock of all classes having a preference upon
the distribution of the corporations assets. In addition, the payment of
distributions to shareholders is subject to any prior rights of outstanding preferred
stock.

Preferred Stock

This
section describes the general terms and provisions of our preferred stock. We have
incorporated by reference our certificate of incorporation as an exhibit to the
registration statement. Because this is a summary, it does not contain all of the details
found in the full text of our certificate of incorporation. If you would like additional
information you should read our certificate of incorporation.

General

Under
our articles of incorporation, the Company may issue from time to time shares of preferred
stock in one or more series and with such relative rights and preferences and at such
times and for such consideration as the board of directors may determine.

The
board of directors may determine the following for each series of preferred stock:

| |  | the
number of shares and designation of the series;
|- |  | ---------------------------------------------------

| |  | dividend
rights;
|- |  | ----------------

| |  | whether
and upon what terms the shares will be redeemable;
|- |  | ----------------------------------------------------------

| |  | whether
and upon what terms the shares will have a sinking fund to be used to purchase or redeem
the                   shares of any series;
|- |  | --------------------------------------------------------------------------------------------------------------------------------------------

| |  | whether
and upon what terms the shares will be convertible;
|- |  | -----------------------------------------------------------

| |  | the
restrictions, if any, on the issue or reissue of any additional preferred stock,
including increases or decreases in the number of shares of any series subsequent to the
issue of shares of that series;
|- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| |  | the
rights of the holders of the shares of any series upon dissolution or the distribution of
our assets; and
|- |  | -------------------------------------------------------------------------------------------------------------

| |  | the
voting rights, if any, which will apply.
|- |  | --------------------------------------------

-8-

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Senior Convertible Preferred Stock

On
July 23, 1998, the Company issued $7.5 million, or 7,500 shares, of
Senior Convertible Preferred Stock. These shares were initially convertible, at
the option of the holders, into shares of our common stock at a price equal to
$8.50 per share of common stock. The August 1999 issuance of Series B
Convertible Preferred Stock, discussed below, triggered antidilution provisions
of the Senior Convertible Preferred Stock, which resulted in a decrease in the
conversion price of those shares from $8.50 to $8.14 per share. The shares of
Senior Convertible Preferred Stock bear a dividend of 7.5% per annum, payable
semiannually. During the first two years, these dividends were paid by issuing
additional shares of Senior Convertible Preferred Stock, which resulted in a
total of 8,706 shares currently outstanding. After July 2000, the Company has
the option to pay the dividend either in cash or by issuing our common stock
valued at the then current market price. At the Companys option, upon
maturity in July 2008, the shares of Senior Convertible Preferred Stock either
must be (a) converted into our common stock, subject to a $3.0 million
conversion fee payable in cash or by issuing additional shares of common stock,
or (b) redeemed for cash at $1,000 per share plus accrued dividends. The
holders of the Senior Convertible Preferred Stock are entitled to designate an
individual to serve on our board of directors, and Michael Greene serves as that
designated board member.

The
holders of the Senior Convertible Preferred Stock are entitled to vote on all matters
submitted to our stockholders for a vote. The holders of the Senior Convertible Preferred
Stock vote with the holders of common stock together as a single class with each share of
Senior Convertible Preferred Stock entitled to one vote for each share of common stock
issuable upon conversion of the Senior Convertible Preferred Stock. In addition, the
Company cannot take any of the following actions without first obtaining the affirmative
vote or written consent of holders of a majority of the shares of Senior Convertible
Preferred Stock: liquidate, wind up, dissolve, merge or consolidate the Company, sell all
or substantially all of the assets of the Company, pay dividends to holders of common
stock, incur indebtedness that would cause our aggregate indebtedness (excluding
indebtedness that is secured by accounts receivable) to exceed two and one-half times the
Companys net income before interest expense, depreciation, amortization and taxes
for the preceding four calendar quarters, or issue equity securities for less than the
conversion price other in a public offering or certain other permitted issuances.

Series B Convertible Preferred Stock

On
August 2, 1999, the Company issued $2.95 million, or 2,950 shares, of
Series B Convertible Preferred Stock. These shares are convertible, at the
option of the holders, into shares of our common stock at a price equal to $6.50
per share of common stock. The shares of Series B Convertible Preferred
Stock bear a dividend of 7.5% per annum, payable semiannually. The Company has
the option to pay, and to date has paid, these dividends by issuing additional
shares of Series B Convertible Preferred Stock, which resulted in a total
of 4,106 shares currently outstanding. At the Companys option, upon
maturity in August 2009, the shares of Series B Convertible Preferred Stock
either must be (a) converted into our common stock, subject to a
$1.2 million conversion fee payable in cash or by issuing additional shares
of common stock, or (b) redeemed for cash at $1,000 per share plus accrued
dividends.

The
holders of the Series B Convertible Preferred Stock are not entitled to any voting rights.

-9-

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Warrants for the Purchase
of Series C Convertible Preferred Stock and Series D Non-Voting Preferred Stock

In
connection with the August 1999 issuance of Series B Convertible Preferred
Stock, the Company issued two seven-year warrants. One of the warrants entitles
the holders to receive, upon payment of a $2.05 million exercise price, either
(a) 2,050 shares of Series C Convertible Preferred Stock, or
(b) 315,385 shares of Series D Non-Voting Preferred Stock, or
(c) a combination of Series C Convertible Preferred Stock or
Series D Non-Voting Preferred Stock. The Series C Convertible
Preferred Stock is similar to the Series B Convertible Preferred Stock
except that it is convertible into shares of the Series D Non-Voting
Preferred Stock at a conversion price of $6.50 per share. The Series D
Non-Voting Preferred Stock is equivalent to our common stock except that it has
no voting rights.

The
second warrant entitles the holder to purchase 282,353 shares of Series D
Non-Voting Preferred Stock at an exercise price of $4.25 per share.

Both
warrants are currently outstanding and neither has been exercised.

Transfer Agent and Registrar

The
transfer agent and registrar for the Company is Wells Fargo Bank Minnesota, N.A.,
Minneapolis, Minnesota.

-10-

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# PLAN OF DISTRIBUTION

We
may sell or distribute some or all of our respective shares of common stock from time to
time in one or more transactions:

| |  | directly to purchasers in transactions (which may involve crosses and block transactions) on the Nasdaq
         National Market, in privately negotiated transactions or in the over-the-counter market;
|- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| |  | through dealers, brokers or other agents;                                                                                                                                                                
| |  | through underwriters; or                                                                                                                                                                                 
| |  | through a combination of any of the above.                                                                                                                                                               

Such transactions may be effected:

| |  | at a fixed price or prices, which price or prices may be changed;
|- |  | -----------------------------------------------------------------
| |  | at market prices prevailing at the time of sale;                 
| |  | at prices related to such prevailing market prices; or           
| |  | at negotiated prices.                                            

Brokers,
dealers or other agents participating in such transactions as agents may receive
compensation in the form of discounts, concessions or commissions from us (and, if they
act as agent for the purchaser of the shares, from the purchaser). Such discounts,
concessions or commissions as to a particular broker, dealer or other agent might be in
excess of those customary in the type of transaction involved.

Any
such brokers, dealers or other agents that participate in such distribution may be deemed
to be underwriters within the meaning of the Securities Act of 1933, as
amended, and any discounts, commissions or concessions received by any such brokers,
dealers or other agents might be deemed to be underwriting discounts and commissions under
the Securities Act.

We
will provide a supplement to this prospectus to disclose the specific shares to be sold,
the public offering price of the shares to be sold, the names of any underwriters,
brokers, dealers or other agents employed by us in connection with such sale, and any
underwriting commissions or discounts paid by us.

Any
person engaged in a distribution of the shares of common stock offered by this prospectus
may not simultaneously engage in market activities with respect to our common stock for
the applicable period under Regulation M under the Securities Exchange Act of 1934, as
amended. These provisions may affect the marketability of the shares offered by this
prospectus.

Any
underwriter may engage in over-allotment, stabilizing and syndicate short covering
transactions and penalty bids in accordance with Regulation M. Over-allotment involves
sales in excess of the offering size, which creates a short position. Stabilizing
transactions involve bids to purchase the underlying security so long as the stabilizing
bids do not exceed a specified maximum. Syndicate short covering transactions involve
purchases of securities in the open market after the distribution has been completed in
order to cover syndicate short positions. Penalty bids permit the underwriters to reclaim
selling concessions from dealers when the securities originally sold by such dealers are
purchased in covering transactions to cover syndicate short positions. These transactions
may cause the price of the offered common stock to be higher than it would otherwise be.
These transactions, if commenced, may be discontinued by the underwriters at any time.

-11-

---

Underwriters,
dealers and agents may be entitled, under agreements entered into with us, to
indemnification against and contribution toward certain civil liabilities, including
liabilities under the Securities Act of 1933, as amended, and to reimbursement by us for
expenses.

Certain
of any such underwriters, dealers or agents and their associates may engage in
transactions with and perform services for us in the ordinary course of business.

In
connection with the offer and sale of the shares of common stock by us, various state
securities laws and regulations require that any such offer and sale should be made only
through the use of a broker-dealer registered as such in any state where we engage such
broker-dealer and in any state where such broker dealer intends to offer and sell shares.

Any
common stock sold pursuant to this prospectus will be listed on the Nasdaq National
Market, subject to official notice of issuance.

# LEGAL MATTERS

The
validity of the shares offered by this prospectus has been passed upon for us by Dorsey
& Whitney LLP, Minneapolis, Minnesota.

# EXPERTS

The
financial statements of Orphan Medical, Inc. included in Orphan Medical,
Inc.s Annual Report (Form 10-K/A Amendment No. 3) for the year ended
December 31, 2003, have been audited by Ernst & Young LLP, independent
registered public accounting firm, as set forth in their report thereon included
therein and incorporated herein by reference. Such financial statements are
incorporated herein by reference in reliance upon such report given on the
authority of such firm as experts in accounting and auditing.

# WHERE YOU CAN FIND MORE INFORMATION

Federal
securities law requires us to file information with the Securities and Exchange Commission
concerning our business and operations. We file annual, quarterly and current reports,
proxy statements and other information with the SEC. You can read and copy these documents
at the public reference facility maintained by the SEC at Judiciary Plaza, 450 Fifth
Street, NW, Room 1024, Washington, DC 20549. Please call the SEC at 1-800-SEC-0330
for further information on the public reference rooms. Our SEC filings are also available
to the public on the SECs web site at http://www.sec.gov. You can also inspect our
reports, proxy statements and other information at the offices of the Nasdaq National
Market.

We
have filed with the SEC a registration statement on Form S-3 to register
the common stock to be sold in connection with this prospectus. This prospectus,
which forms a part of the registration statement, does not contain all of the
information included or incorporated in the registration statement. The SEC
allows us to incorporate by reference the information we file with
it, which means that we can disclose important information to you by referring
you to those documents. The information that we incorporate by reference is
considered to be part of this prospectus, and later information that we file
with the SEC will automatically update and supersede this information. We
incorporate by reference the documents listed below and any future filings made
with the SEC (including all filings from the initial filing date through the
termination date of this offering) under Sections 13(a),
13(c), 14 or 15(d) of the Securities Exchange Act of 1934, as amended:

| |  | our Annual Report on
Form 10-K/A (Amendment No. 3), filed July 20, 2004 (Commission File Number 0-24760), for the fiscal year ended
December 31, 2003;
|- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------
| |  | our Quarterly Report on Form 10-Q filed
May 10, 2004 (Commission File Number 0-24760), for the period ended March 31, 2004;                           
| |  | our Current Report on Form 8-K, filed
April 20, 2004 (Commission File Number 0-24760); and                                                            
| |  | our Current Report on Form 8-K, filed
May 24, 2004 (Commission File Number 0-24760).                                                                  

-12-

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Upon
written or oral request, we will provide to each person to whom a copy of this prospectus
is delivered, at no cost, a copy of any of the documents that are incorporated by
reference into this prospectus. You may request a copy of any of the above filings by
writing or telephoning us at the following address:

Timothy G. McGrath,
Chief Financial Officer
Orphan Medical, Inc.
13911 Ridgedale Drive
Suite 250
Minnetonka, Minnesota 55318
(952) 513-6900

-13-

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# PART II.

# INFORMATION NOT REQUIRED
IN PROSPECTUS

# Item 14. Other Expenses
of Issuance and Distribution

|SEC Registration Fee         |  |  | $ | 5,980   | 
|---------------------------- |  |  | - | ------- | 
|Accounting Fees and Expenses |  |  |   | 25,000  | 
|Legal Fees and Expenses      |  |  |   | 75,000  | 
|Miscellaneous                |  |  |   | 14,020 
|Printing Expenses            |  |  |   | 25,000  | 
|Nasdaq Filing Fee            |  |  |   | 5,000  
|                             |  | 
|Total                        |  |  | $ | 150,000 | 
|                             |  | 

All
fees and expenses other than the SEC registration fee are estimated. The expenses listed
above will be paid by Orphan Medical, Inc. (the Company).

# Item 15. Indemnification of Officers and Directors

Section
145 of the Delaware General Corporation Law contains detailed provisions for
indemnification of directors and officers of Delaware corporation against expenses,
judgment, fines and settlements in connection with litigation. Reference is made to
Section 145, which is incorporated herein by reference. The following summary is
qualified in its entirety by that reference.

Delaware
law permits a corporation to indemnify officers and directors against expenses and other
liabilities arising out of legal actions brought or threatened against them, provided that
the officer or director each acted in good faith and did not involve a knowing violation
of the law. Delaware law does not allow indemnification for directors in cases brought
against a director by the corporation or its stockholders unless indemnification is
ordered by a court. Delaware law also permits a corporation to enter into agreement with
officers and directors providing for indemnification against certain liabilities in
addition to indemnification rights permitted by law or in the corporations
certificate of incorporation or bylaws.

Our
bylaws provide that we shall indemnify officers and directors under such circumstances and
to the extent permitted by Section 145 of the Delaware General Corporation Law as now
enacted or hereafter amended.

The
Company has entered into agreements with its directors and executive officers which
provide that the Company shall indemnify such persons to the fullest extent authorized by
the Delaware General Corporation Law. Such agreements also set forth certain procedures
with regard to advances, settlement, maintenance of insurance, notification of claims and
defense of claims.

The
Company maintains a standard policy of directors and officers liability
insurance.

# Item 16. List of Exhibits

1.1
Form of Underwriting Agreement (to be filed by amendment or by Current Report on Form 8-K
pursuant to Item 601(b) of Regulation S-K).

4.1
Specimen of Common Stock Certificate (incorporated by reference to Exhibit 4.1 to the Companys
Registration Statement on Form S-3 (No. 333-51287), filed with the Commission on April 29, 1998, as
amended through the date hereof).

5.1 Opinion of Dorsey & Whitney LLP regarding legality (previously filed).

23.1 Consent of Ernst & Young LLP.

II-1

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23.2
    Consent of Dorsey & Whitney LLP (included in Exhibit 5.1).

24.1
    Power of attorney from directors of Orphan Medical, Inc. (included on the signature
page in the initial filing).

# Item 17. Undertakings

The
undersigned registrant hereby undertakes:

| | (1)       
               To file, during any period in which offers or sales are being made, a
               post-effective amendment to this registration statement:
| | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (i)       
               To include any prospectus required by section 10(a)(3) of the Securities Act of
               1933;
| | ------------------------------------------------------------------------------------------------------------------------------

| | (ii)       
               To reflect in the prospectus any facts or events arising after the effective
               date of the registration statement (or the most recent post-effective amendment
               thereof) which, individually or in the aggregate, represent a fundamental change
               to such information in the registration statement. Notwithstanding the
               foregoing, any increase or decrease in volume of securities offered (if the
               total dollar value of securities offered would not exceed that which was
               registered) and any deviation from the low or high end of the estimated maximum
               offering range may be reflected in the form of prospectus filed with the
               Commission pursuant to Rule 424(b) under the Securities Act if, in the
               aggregate, the changes in volume and price represent no more than a 20% change
               in the maximum aggregate offering price set forth in the Calculation of
               Registration Fee table in the effective registration statement; and
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (iii)       
               To include any material information with respect to the plan of distribution not
               previously disclosed in the registration statement or any material change in the
               information set forth in the registration statement;
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | provided,
however, that paragraphs (1)(i) and (1)(ii) do not apply if the registration statement
is on Form S-3 or Form S-8, and the information required to be included in a
post-effective amendment by those paragraphs is contained in periodic reports filed by the
registrant pursuant to section 13 or section 15(d) of the Securities Exchange Act of 1934
that are incorporated by reference in the registration statement.
| | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (2)       
               That, for the purpose of determining any liability under the Securities Act of
               1933, each such post-effective amendment shall be deemed to be a new
               registration statement relating to the securities offered therein, and the
               offering of such securities at that time shall be deemed to be the initial bona
               fide offering thereof.
| | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (3)       
               To remove from registration by means of a post-effective amendment any of the
               securities being registered which remain unsold at the termination of the
               offering.
| | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | The
undersigned registrant hereby undertakes that, for purposes of determining any liability
under the Securities Act of 1933, each filing of the registrants annual report
pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 that is
incorporated by reference in the registration statement shall be deemed to be a new
registration statement relating to the securities offered therein, and the offering of
such securities at that time shall be deemed to be the initial bona fide offering
thereof.
| | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | Insofar
as indemnification for liabilities arising under the Securities Act of 1933 may be
permitted to directors, officers, and controlling persons of the registrant pursuant to
the foregoing provisions, or otherwise, the registrant has been advised that, in the
opinion of the Securities and Exchange Commission, such indemnification is against public
policy as expressed in the Act and is, therefore, unenforceable. In the event that a
claim for indemnification against liabilities (other than the payment by the registrant
of expenses incurred or paid by a director, officer or controlling person of the
registrant in the successful defense of any action, suit or proceeding) is asserted by
such director, officer or controlling person in connection with the securities being
registered, the registrant will, unless in the opinion of its counsel the
| | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

II-2

---

| | matter has been settled by
controlling precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the Act and will be
governed by the final adjudication of such issue.
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

II-3

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# SIGNATURES

Pursuant
to the requirements of the Securities Act of 1933, the registrant certifies that it has
reasonable grounds to believe that it meets all of the requirements for filing on Form S-3
and has duly caused this Registration Statement to be signed on its behalf by the
undersigned, thereunto duly authorized, in the City of Minnetonka, State of Minnesota, on
July 20, 2004.

| | ORPHAN MEDICAL, INC.                       
| | -------------------------------------------
|
| | By: /s/ John Howell Bullion                
| |                                            
| | John Howell Bullion
Chief Executive Officer

Pursuant to the requirements of the
Securities Act of 1933, this Registration Statement has been signed by the following
persons in the capacities and on the date indicated.

|Name                                               | Title                                        | Date         
|-------------------------------------------------- | -------------------------------------------- | -------------
|                                                  
|/s/ John Howell Bullion                            | Chief Executive Officer, Director and        | July 20, 2004
|                                                   | Chairman of the Board                        |              
|John Howell Bullion                                | (Principal Executive Officer)               
|                                                  
|/s/ Timothy G. McGrath                             | Chief Financial Officer (Principal Financial | July 20, 2004
|                                                   | Officer and Principal Accounting Officer)    |              
|Timothy G. McGrath                                
|                                                  
|*                                                  | Director                                     | July 20, 2004
|                                                  
|Michael Greene                                    
|                                                  
|*                                                  | Director                                     | July 20, 2004
|                                                  
|Julius A. Vida, Ph.D                              
|                                                  
|*                                                  | Director                                     | July 20, 2004
|                                                  
|William M. Wardell, M.D., Ph.D                     |                                             
|                                                  
|*                                                  | Director                                     | July 20, 2004
|                                                  
|Thomas B. King                                    
|                                                  
|*                                                  | Director                                     | July 20, 2004
|                                                  
|Farah H. Champsi                                  
|                                                  
|*By:  /s/ John Howell Bullion                      |                                              |              
|                                                  
|John Howell Bullion            as attorney-in-fact



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# EXHIBIT INDEX

|Exhibit No. | Description
|----------- | -----------
|           
|1.1         |            
|4.1         |            
|5.1         |            
|23.1        |            
|23.2        |            
|24.1        |            

II-2

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