Objectives: Streptococcus pneumoniae causes acute otitis media, pneumonia, meningitis and bacteraemia. This study aimed to determine the prevalence of Streptococcus pneumoniae oropharyngeal carriage in healthy children and the antimicrobial susceptibility in a daycare nursery and a government-managed orphanage in Kuala Lumpur during 2010.Methods: Throat swabs were obtained from 36 children of daycare nursery (open community) and from 84 orphans from orphanage (closed community) those did not receive any pneumococcal vaccine. Children were between births to 6 years of age. Antibiotic susceptibility of isolated strains was determined using disk diffusion method and Etest� (minimum inhibitory concentration). Results: Overall prevalence of Streptococcus pneumoniae of the children was 1.7% (2 out of 120). Prevalence of the bacteria in open community was 5.6% (2 out of 36) and no positive cases were recorded in orphanage (closed community, (p=0.161). Prevalence was 15.4% (2 out of 13) in children aged below 2 years in the open community. There was no association was found to exist between Streptococcus pneumoniae carriage with age (p=0.432) and gender (p=0.418). Serotyping showed serotype 11F for one isolate, while the other was non-typable. Both isolates were susceptible to penicillin, azithromycin, ceftriaxone and vancomycin. The serotype 11F isolate was susceptible while the non-typable isolate was resistant to erythromycin.Conclusions: The results demonstrated low prevalence of Streptococcus pneumoniae in healthy children. These findings may complement other studies to explore further risk factors for colonisation, antimicrobial susceptibility and serotype distribution of Streptococcus pneumoniae to help for the planning of immunization strategies.