Exhibit 31.1

# CERTIFICATIONS

I, John H. Bullion, Chief Executive Officer of Orphan
Medical, Inc., certify that:

|1. |  | I have reviewed this Quarterly Report on Form 10-Q of Orphan Medical, Inc.;
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|2. |  | Based on my knowledge, this report does not contain any untrue statement of a
material fact or omit to state a material fact necessary to make the statements
made, in light of the circumstances under which such statements were made, not
misleading with respect to the period covered by this report;
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|3. |  | Based on my knowledge, the financial statements, and other financial information
included in this report, fairly present in all material respects the financial
condition, results of operations and cash flows of the registrant as of, and
for, the periods presented in this report;
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|4. |  | The registrants other certifying officer(s) and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:
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|a) |  | Designed such disclosure controls and procedures, or caused such disclosure
controls and procedures to be designed under our supervision, to ensure that
material information relating to the registrant, including its consolidated
subsidiaries, is made known to us by others within those entities, particularly
during the period in which this report is being prepared;
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|b) |  | Evaluated the effectiveness of the registrants disclosure controls and
procedures and presented in this report our conclusions about the effectiveness
of the disclosure controls and procedures, as of the end of the period covered
by this report based on such evaluation; and
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|c) |  | Disclosed in this report any change in the registrants internal control
over financial reporting that occurred during the registrants most recent
fiscal quarter (the registrants fourth fiscal quarter in the case of an
annual report) that has materially affected, or is reasonably likely to
materially affect, the registrants internal control over financial
reporting; and
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|5. |  | The registrants other certifying officer(s) and I have disclosed, based on
our most recent evaluation of internal control over financial reporting, to the
registrants auditors and the audit committee of the registrants
board of directors (or persons performing the equivalent functions):
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|a) |  | All significant deficiencies and material weaknesses in the design or operation
of internal control over financial reporting which are reasonably likely to
adversely affect the registrants ability to record, process, summarize and
report financial information; and
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|b) |  | Any fraud, whether or not material, that involves management or other employees
who have a significant role in the registrants internal control over
financial reporting.
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|Date:   August 9, 2004 |  | /s/   John H. Bullion   | 
|---------------------- |  | ----------------------- | 
|                       |  |                        
|                       |  | Chief Executive Officer

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