Four genera of microsporidia have been associated with disease in humans, which predominantly affects immunocompromised persons. Systemic infection with a newly characterized microsporidian species, Encephalitozoon hellem, was recently reported in a patient with AIDS. This article describes a second patient with AIDS and disseminated E. hellem infection. In this case the parasite was detected in sputum, urine, and conjunctival swab specimens. Apart from recurrent mild conjunctivitis and asymptomatic microhematuria, the patient had no findings or symptoms that could be related to this parasite. Specifically, no microsporidian-associated pulmonary pathology was documented. Detection of E. hellem in the patient's sputum may have epidemiological implications in that this finding suggests transmission of microsporidia by the aerosol route. Because the patient died of unrelated complications, it remains unknown whether he was an asymptomatic carrier of microsporidia or whether microhematuria heralded early microsporidian disease, with the onset of cellular damage in the urinary tract.