A prospective study was carried out to determine the prevalence rates of microsporidiosis and other enteroparasites in HIV-positive children in the Madrid area. HIV-positive pediatric patients from three hospitals were enrolled in the study. A total of 293 samples (158 stool and 127 urine) were collected from 83 children whose mean age was 6.3 years and had a mean CD4 count of 504.7/mm3 (range 1-2,220/mm3), 48 of whom suffered diarrhea at the time of the study. Microsporidia identification was investigated in stool and urine samples using Weber's chromotrope-based stain, IIF and PCR species-specific tests. Enteric parasites were identified in 32.5% of the children. Cryptosporidium sp. was the most common parasite encountered (14.4%), followed by Blastocytis sp. (9.6%) and Giardia duodenalis (8.4%). Microsporidia was only found in the stools of one child (1.2% of total and 2% of those with diarrhea) and Enterocytozoon bieneusi was demonstrated by PCR. The patient was 10 years old, presented non-chronic diarrhea and his CD4 count was 298/mm3. These data differ from those previously reported by us in HIV-positive adults (13.9%) in the same area, although this group showed more severely depressed CD4 lymphocyte counts than children. New epidemiological studies should be carried out to elucidate whether additional risk factors exist between these groups.