A study was conducted between 1993 and 1996 in Bamako to determine the rate of occurrence of microsporidia in 88 patients. Most (80%) had chronic diarrhea associated with weight loss and 87.5% were HIV-positive. Intestinal microsporidia were detected in 32% of the patients infected with HIV-1, HIV-2, or coinfected with both strains. Microsporidiosis was also diagnosed in three of the eleven HIV-negative individuals (27%). Microsporidiosis was confirmed by electron microscopy in 6 HIV-positive patients and 1 HIV-negative individual. Enterocytozoon bieneusi was detected in each case. These results suggest that microsporidia are common pathogens in HIV-positive patients in Bamako. Cases of microsporidiosis have been reported for the first time in HIV-2-infected patients. The proportion of women microsporidiosis patients is higher in Mali than in industrialized countries. The presence of microsporidia in HIV-negative patients suggests that these parasites may be an underestimated cause of enteritis in developing countries.