This study documents the colonization of Staphylococcus aureus (SA), Streptococcus pneumoniae (SP) and specific resistant forms of these organisms among healthy children and identifies risk factors associated with these pathogens. Prospective point prevalence survey of nasopharyngeal specimens were obtained from 291 healthy children seeking routine well-child care at a university-based ambulatory paediatric clinic in a large urban city in the United States. A total of 291 children less than 5 years were enrolled during a 1-year period. Fifty-four (18·6%) were colonized with SA and 47 (16·2%) were colonized with SP. Among the 54 SA isolates, five (9·2%) were methicillin resistant (MRSA) and among the SP isolates, three (6·4%) were intermediate to penicillin (DRSP). Eighty per cent of all children enrolled reported no underlying medical condition. Care outside their home was more common among colonized (40·8%, 40/98) than non-colonized children (25·4%, 49/193), P=0·007. Healthy children from households of four or more people were also more likely to be colonized. The colonization rate of SA and SP among healthy children is consistent with what has been reported in the literature. The prevalence of MRSA and DRSP among healthy children colonized with SA or SP is low in this population of children attending a university-based ambulatory care centre in the United States.