Microsporidiosis is an increasingly important opportunistic infection in HIV-positive patients. Five species of microsporidia {Enterocytozoon bieneusi, Encephalitozoon hellem and E. cunieuli, Seplata intestinalis, and Pleistophora sp.) have been reported to occur in AIDS, with each agent producing a different clinicopathologic spectrum of disease. This communication reviews routine and specialized methods for diagnosis of these important pathogenic protozoa, including biopsy, cytology, ultrastructural and immunologic examination, and tissue culture, and describes the current knowledge of organ distribution for microsporidia in persons with AIDS.