To determine the frequency of the parasitic pathogens in human immunodeficiency virus (HIV)-infected patients in a developing world setting, 295 stool specimens were examined from 166 HIV-positive patients (49% with AIDS) at São José Hospital, Fortaleza, Brazil, from September 1990 to March 1992. Significantly more patients with diarrhea (85%) than without (66%) had AIDS or AIDS-related complex (ARC) (P < .005). Of the potential parasitic causes of diarrhea, only Cryptosporidium parvum and microsporidia were significantly associated with diarrheal disease. Infections with C. parvum, but not microsporidia, were associated with the rainy season (P < .005). Thus, C. parvum and microsporidia are the most common intestinal parasites associated with diarrhea in an HIV-infected population in Brazil and are associated with advanced HIV disease. The association of C. parvum infections with the rainy season suggests that contaminated water may be important in its transmission; however, the source of human microsporidia requires further investigation.