Congenital heart defects represent 25% of all congenital malformations and threaten nearly 1% of all newborns and pose a significant threat of infant death. Cardiac development during embryogenesis has been linked to the zinc finger transcription factor GATA4 (found on chromosome 8p23.1) and the T-box transcription factor family member TBX5 (placed on chromosome 12q24.21). Mutations in the GATA4 and TBX5 genes have been implicated in the development of various congenital cardiac disorders. To detect the mutations in GATA4 and TBX5 genes in children with congenital heart diseases by using direct sequencing technique. Methods: Thirty children with congenital heart disorders were studied, and their results were compared to thirty apparently healthy children with matching age and sex and without a family history of cardiac diseases as a control group. All patients underwent clinical examination, echocardiography, and genetic testing for the GATA4 rs55633527, GATA4 rs114868912, and TBX5 rs77357563 polymorphisms using the Sanger sequencing method, as well as other tests. Two variants were detected in GATA4 gene and one variant in TBX5 gene. Conclusions: GATA4 1 rs55633527 CT+TT, GATA4 2 rs114868912 GA+AA and TBX5 rs77357563 GT +TT were significantly associated with higher risk to develop congenital heart disease.