Stool specimens submitted to Charity Hospital and the HIV Outpatient Clinic, New Orleans, LA from HIV-infected individuals with abdominal pain and/or chronic diarrhea were examined for the presence of microsporidia by histochemistry (modified trichrome staining and calcofluor staining) and PCR-based methods. In addition, survey questionaire results and clinical chart data were evaluated to assess demographics, risk factors, and natural history of microsporidiosis. Of 265 stool specimens examined, 41 (15.5%) were positive for microsporidia and 78 % of the positive specimens were collected during the summer months (May - August). Those persons with < 100 CD4+ T cells/fl blood were more likely to continue shedding microsporidia and experiencing clinical manifestations at the six-month follow-up examination, than persons with higher CD4+ T cell levels who were more likely to resolve their microsporidial infections. One risk factor identified for microsporidiosis was exposure to freshwater or seawater fish. Microsporidiosis is believed to be zoonotic since several species of microsporidia identified in humans also are known to infect other animals. Additional evidence to support this hypothesis includes the identification of Encephalitozoon cuniculi strain III (originally identified in domestic dogs) in AIDS patients in the U.S.A., and Encephalitozoon hellem, which had only been identified in AIDS patients, was recently identified in psittacine birds in an aviary in Mississippi and from archival avian tissues in Texas. A new Encephalitozoon species is being characterized in African lizards (skinks), and E. cuniculi strain I has been identified in the lens of a rabbits, suggesting that congenital transmission of microsporidiosis can occur in this host. Studies will continue to characterize new species of microsporidia that may infect humans and to identify zoonotic risks of microsporidiosis in humans.