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Among 1454 persons whose stool samples (n =5692) were submitted to a reference laboratory for microsporidia assessment from 1993 to 1996, microsporidia were identified in 338 persons: 261 persons infected with human immunodeficiency virus (HIV), 16 transplant patients, and 61 others. Intestinal microsporidiosis appears to be an endemic disease in HIV-positive persons (prevalence, 0.1%) and a sporadic disease in HIV-negative persons (prevalence, <1/1 million). A waterborne outbreak in 200 persons (attack rate, 1% in HIV-positive patients/month) occurred in the 1995 summer, without evidence of fecal contamination of water. No explanation was found before the outbreak ended, several months before the antiprotease era. Factors associated with microsporidiosis diagnosis were HIV infection, male homosexuality, low CD4 cell counts, and diarrhea. The major factor associated with a diagnosis of microsporidiosis during the outbreak was living in an area corresponding to one of the three water distribution subsystems of the town. Lake contamination was suspected. [ABSTRACT FROM AUTHOR]