Objective: The prevalence of Streptococcus mutans serotype k, which was speculated that might be associated with the development of cardiovascular diseases, has been reported in adult cardiovascular surgery patients. There is no information about presence of serotype k in children with cardiac disease. The aim of this study was to determine the salivary prevalence of S.mutans serotype k in children with congenital heart disease. Study Design: Salivary samples of 25 patients undergoing elective surgery for congenital heart defects with cardiopulmonary bypass and an age and gender matched control group of 25 healthy children were enrolled in the study. Species-specific 16SrRNA gene sequences were used for S. mutans and serotype-specific rgpF gene sequences were used for S.mutans serotype k determination in stimulated saliva samples. Results: S.mutans was detected in 19 (76%) of the study and 15 (60%) of the control children. The difference was not shown to be statistically significant. Serotype k was determined from 3 (12%) of the study group, while it was not determined from the samples of the control group. Conclusions: Our results indicate that those children with congenital heart disease may possess S.mutans serotype k in oral cavity at a higher frequency as similar with the adult cardiac surgery patients.