Staphylococcus aureus (S. aureus) is occasionally a normal inhabitant of the gastrointestinal tract, and rarely considered a cause of enterocolitis. Methicillin-resistant Staphylococcal enterocolitis may cause persistent diarrhea leading to severe complications and even death, without appropriate treatment. Lymphocytic colitis (LC), a subtype of microscopic colitis, is a relatively common cause of chronic watery diarrhea. We report the case of a 73-year-old woman with profuse watery diarrhea caused by methicillin-resistant S. aureus . Soon after treatment of her enterocolitis with vancomycin the patient's general condition and symptoms improved, although the diarrhea persisted. Through colonoscopic biopsy and immunohistochemical staining, overt LC was diagnosed, and prompt therapy with budesonide was initiated.