HIV-infected children are more likely than other children to develop pneumonia, which in these children is often recurrent or persistent. The main reservoir of the major pathogens is the nasopharynx, but to date no data has been published on the frequency and biologic characteristics of S.pneumoniae, H.influenzae and respiratory viruses found in the upper respiratory tract of children born to human immunodeficiency virus-infected mothers. To document these aspects, 105 children was monitored by pharyngeal swab (PS) and nasopahryngeal aspirates (NPA) who attended an outpatient clinic for HIV-infection evaluation. Bacterial identification was performed by standard procedures. Serotype, biotype and beta-lactamase production was investigated in H.influenzae isolates. S.pneumoniae serotypes were recognized by "quellung" and the susceptibility to 4 antibiotics was assessed. Respiratory syncytial viruses, parainfluenza, influenza A and B, and adenoviruses were diagnosed by indirect immunofluorescence and/or viral isolation in cell cultures. Twenty-nine children were identified as infected by HIV as a result of maternal-child transmission. Seventy children born to HIV-positive mothers but who were not HIV-infected served as controls. Of 269 PS, 110 110 S. pneumoniae and 92 H.influenzae were identified. Also 31 viruses were detected in 188 NPA. After stratifying by age no differences were observed in the frequency of bacterial colonization or in the presence of viruses in the upper respiratory tract of the two groups. Some biologic characteristics of the agents were noteworthy such as the frequency of colonization by S.pneumoniae serotype 14, the predominance of H.influenzae biotype I and the high frequency of viruses in NPA of asymptomatic children. Of note, although colonization frequencies were similar, children presenting with acute respiratory illness (ARI) were more likely to have bacteria isolated if they also had HIV-infection than if they were HIV-negative. It is concluded that HIV-infection in infants as a result of maternal virus transmission have a similar frequency of bacteria and virus colonization of their respiratory tract, but a higher frequency of ARI and perhaps a higher frequency of types of bacteria with special characteristics.