Microsporidia are protozoan parasites responsible for significant gastrointestinal disease in patients infected with human immunodeficiency virus. We report the clinical features of 20 patients with chronic diarrhea for whom microsporidian spores were identified by modified trichrome staining of stool smears and confirmed by biopsy and/or electron microscopy of stool. Of the 18 microsporidian protozoa identified to the species level, 14 (78%) were Enterocytozoon bieneusi and four (22%) were Septata intestinalis. The mean CD4 count in these patients was 35 +/- 29 cells/mm3. Parameters of absorption, specifically absorption of fat and D-xylose, and levels of zinc were strikingly abnormal in patients who were tested. Treatment with albendazole led to clinical responses in six of 10 patients, and dietary manipulation resulted in clinical improvement in eight of nine patients. We recommended that patients with chronic, intermittent diarrhea and CD4 counts of < 100 cells/mm3 be further evaluated for microsporidia by modified trichrome staining of stool and light and electron microscopy of small bowel biopsy specimens. Antiprotozoal therapies are currently experimental, but some patients who have been treated with these therapies have dramatic responses. We also recommend that special attention be paid to the measurement of parameters of absorption with appropriate modification of diet.