To date, the only microsporidian that has been associated with diarrhea and weight loss in acquired immunodeficiency syndrome patients is the newly identified Enterocytozoon bieneusi. A second species is now described that was associated with intestinal symptoms in a 32-year-old, human immunodeficiency virus- seropositive, Native American male homosexual. Stool studies and routine light microscopy of multiple small intestinal biopsies that showed atrophy with acute and chronic inflammation were without apparent pathogens. Light microscopy of semi-thin plastic sections, cytochemical stains of paraffin sections, and ultrastructural studies revealed extensive microsporidial infection of enterocytes and submucosal macrophages. No other pathogens were identified. Unlike E bieneusi, this microsporidian appeared to develop within septated parasitophorous vacuoles, and lacked polar disks and clear clefts. It most closely resembled, but was distinguishable from, members of the genus Encephalitozoon. Awareness of the microsporidia as potential opportunists in acquired immunodeficiency syndrome patients is increasing the incidence of identification of these organisms.