Nasal and rectal cultures were taken from all patients with methicillin-resistant Staphylococcus aureus identified on routine cultures obtained because of clinical indications. Of 117 patients studied over a 3-year period, 70 (60%) had rectal colonization and 62 (53%) had nasal colonization. Rectal colonization, probably reflecting gastrointestinal carriage, may be a source of transmission of methicillin-resistant S. aureus in hospitalized patients and may be difficult to eradicate.