Background and aims. In the presence of certain systemic diseases, oral microflora may aggravate the condition of the disease. Microbial population in the oral cavity especially with heart disease can increase the risk of bacterial endocarditis. The aim of this study was to evaluate the rate of oral Streptococcus mutansand the rate of caries in children suffering from heart disease.Materials and methods. In this cross-sectional research, 66 children with congenital or acquired heart disease and 50 healthy children were selected. Children were orally examined and decayed, missing, and filled teeth (DMFT) index was recorded for each subject. Saliva samples were taken from all subjects, and cultured on a special laboratory media and another specific media for S. mutans (sorbitoll +manitol). Bacterial counts were recorded, and for statistical analysis, chi square, Pearson’s, and Exact Fisher tests were performed using SPSS 16 software.Results. The rate of S. mutans in children with congenital heart disease was significantly higher than the rates in childrenwith acquired heart disease and healthy control subjects. The mean DMFT in children with acquired heart disease who tookpenicillin as prophylaxis monthly was significantly lower than the other groups.Conclusion. The results revealed lower oral bacteria counts and comparatively lower caries rates in children with heart diseases, probably because of an effect of the regular prophylactic antibiotic regimen.