To assess the zoonotic potential of Encephalitozoon-like microsporidia, we isolated and cultivated spores from specimens of urine, respiratory secretions, and stool from six patients infected with human immunodeficiency virus and from nine rabbits. Because spores of Encephalitozoon-like species are indistinguishable by microscopy, we characterized the isolates by western blot analysis and by restriction enzyme analysis of the small subunit (SSU) rDNA after amplification by the polymerase chain reaction. We identified Septata intestinalis in one patient and Encephalitozoon hellem in two symptomatic patients. Encephalitozoon cuniculi was found in all rabbits and in three patients. One of these patients had clinical manifestations of infection with this parasite (severe interstitial pneumonitis). We observed abatement of symptoms and cessation of parasite excretion when these patients were treated with albendazole. Our findings suggest that E. cuniculi may be pathogenic in humans and that it is a zoonotic parasite.