The microsporidian protozoan organism Enterocytozoon bieneusi has been found in enterocytes of the small intestine in patients infected with human immunodeficiency virus, and it has been recognized as an important cause of chronic diarrhea in this patient group. We report the first case of a 41-yr-old man with acquired immunodeficiency syndrome in whom microsporidia were detected in bronchoalveolar lavage fluid, transbronchial lung biopsies, stool specimens, and ileal biopsies. He experienced chronic diarrhea, wasting syndrome, chronic cough, and dyspnea. His chest roentgenogram showed a small left posterobasal infiltrate and a small left pleural effusion. The histologic pattern of microsporidia in his bronchial and ileal tissue and the cellular inflammatory reaction with intraepithelial infiltration by lymphocytes were identical to findings described in duodenal and jejunal Enterocytozoon bieneusi microsporidiosis. An association between the presence of microsporidia in the lung and the pulmonary symptoms has yet to be determined. It is not known whether pulmonary microsporidiosis was acquired by the aerosol route, by aspiration, or by hematogenous dissemination from the intestine.