We present here the frequency of enteropathogens in an HIV-infected children group and investigate their correlation with clinical and sociodemographic characteristics by collecting 100 stool samples from 55 HIV-seropositive Brazilian children. All specimens were processed according to standard methods for bacterial and yeast detection. A commercially available enzyme-linked immunosorbent assay was used to detect protozoan, and to perform virus detection, molecular tests were applied. Consumption of raw vegetables and fruits and severe immunosuppression were significantly associated with diarrhea. Cryptosporidium parvum was the commonest enteropathogen, followed by Candida albicans, enteropathogenic Escherichia coli, and astrovirus. The number of potential pathogenic agents identified in fecal specimens in asymptomatic HIV-seropositive infants is high, which raises the need for additional investigation in this area as well as in other Brazilian regions.