© 2017 Indian Journal of Dental Research | Published by Wolters Kluwer-Medknow.Aim: The purpose of this study was to analyze the presence of Aggregatibacter actinomycetemcomitans in saliva and cardiac tissue samples of children requiring cardiac surgery in Istanbul, Turkey. Subjects and Methods: Twenty-five patients (mean age: 6.24 ± 2.93) undergoing surgery for congenital heart defects (CHDs) and an age/gender-matched control group of 25 healthy children were enrolled in the study. Saliva samples were collected from all children; plaque index (PI) and gingival index (GI) were also determined. In CHD group, cardiac tissue samples were received during surgery. All samples were evaluated for the presence of A. actinomycetemcomitans and its highly leukotoxic JP2 clonal strains using polymerase chain reaction. The findings were analyzed by Mann-Whitney U, Chi-square, and Fisher's exact tests. Results: No significant differences were found in PI and GI values between the groups. A. actinomycetemcomitans was not detected in cardiac tissue samples. A. actinomycetemcomitans in saliva was detected in 2 (8%) of the CHD and 5 (20%) of the control children (p > 0.05). A. actinomycetemcomitans JP2 clonal strains were determined from 1 (4%) of the control group while it was not determined from the samples of the CHD group. Conclusions: Early colonization of A. actinomycetemcomitans in oral cavities could be assessed as a risk marker for periodontal disease. Periodontal pathogens may enter bloodstream through bacteremia; thus, the presence of periodontal pathogens in the oral cavity of children should be assessed as a risk marker for cardiac diseases in older ages.