A 39-year-old patient with acquired immunodeficiency syndrome was diagnosed as having intestinal Enterocytozoon bieneusi microsporidiosis after persistent watery diarrhea for 30 months and a 16-kg weight loss. Microsporidian parasites were found by light and electron microscopy in tissue specimens of the duodenum, jejunum, and terminal ileum, and by light microscopic examination of stool specimens. When duodenal tissue sections obtained 16 months previously were reviewed retrospectively, E. bieneusi was also found. Until now, diagnosis of intestinal microsporidiosis has been based on examination of bioptic specimens of the upper small intestine because the sensitivity of new coprodiagnostic techniques has not been determined. Our findings of ileal microsporidiosis show that examination of the terminal ileum and ileal biopsy collection in tandem with colonoscopy is indicated for patients infected with human immunodeficiency virus and suffering from unexplained chronic diarrhea. The long-term course of our patient demonstrates that E. bieneusi, although not necessarily life threatening, can cause protracted debilitating diarrhea and wasting in severely immunodeficient patients.