Introduction: In the present study, we aimed to investigate of Myocyte enhancer factor 2C (MEF2C) gene polymorphisms on the children with Down syndrome, compare them with healthy controls and determine its relationship between cardiac malformations which are common by Down syndrome.

Materials and Methods: A hundred pediatric patients with Down syndrome and 100 healthy children as the control group were included and the primers of related mutation regions were designed and polymorphisms identified in the gene region were investigated with Real Time PCR (real-time polymerase chain reaction) method.

Results: While 58 percent of down syndrome patients were girls 42 percent of patients were boys and their average age was 3.19±3.79. Maternal average age of patieints was found to be 36.86±6.67. It was found that 18% of down syndrome patients, with congenital heart disease, had ventriküler septal defect (VSD), 18% had atrial septal defect (ASD), 11% had patent ductus arteriosus (PDA), 7% had atrioventricular septal defect (AVSD) and 19% had more than a heart defective disease. And it wasn't any heart defects detected on 27% of patients. Gene regions; which are located on MEF2C rs770189, rs4521516,rs11951031, rs12521522, rs17560407, rs17421627 were studied. When comparing the alleles on rs770189,rs4521516 and rs17560407 regions there wasn't any significant difference between patient and control group detected. But, statistically, it was detected that there is a significant difference between rs11951031, rs12521522 and rs17421627 gene regions's alleles (P<0.05).

Conclusion: While It has been found that by patients with down syndrome and congenital heart disease, frequency of the rs 12521522, rs11951031 and rs 17421627 gene regions’ alleles significantly increased; No significance between patients with Down syndrome and with cardiac malformation with normal ecocardiography and Down syndrome was detected.