Congenital cardiac septal defect (CSD) is the most common of congenital heart anomalies. The T-box transcription factor TBX5 gene is important in mammalian cardiac development either cardiac septation or morphogenesis. We aimed in this study to characterize the TBX5 variants in non-HOS patient with CSD. This case-controlled study was conducted on 30 unrelated affected children with non-syndromic isolated and non-isolated cardiac septal defects and 28 apparently healthy children with matching age and sex and without a family history of cardiac diseases as a normal control group. We detected reported intronic variant (g.18738) in 12 cases and coding variant (p.L135R) in one case. These results provide further insight into the pivotal molecular role of Tbx5 variants in cardiac development and pathogencity. This in turn could contribute to the therapeutic strategies for CSD.