Background : Congenital heart diseases (CHD) are the most common of all birth defects, affecting nearly 0.9% of all live births Nkx2-5 mutations were reported to cause CHD but data in Kurdish populations of Iran are limited. Patients and Methods : In this experimental study, we performed High Resolution Melt (HRM) mutation scanning of Nkx2-5 exons of non-syndrome patients, 39 patients with atrial septal defect and 57 ents with ventricular septal defect, 4 patients possessing both defects as case groups and 50 healthy controls Then we grouped samples according to HRM graph and sequenced several samples from each group. Results. : HRM analysis showed 2 deviated curves for exon 1 and one group for exon2A and exon 2B. Then, 2 samples of exon 1 that showed different HRM curves, 3 samples of another group from this exon and 5 samples of exon 2A, 2B and healthy controls were randomly sequenced. The results of sequencing confirmed the HRM analysis, and one polymorphism (A65G) was identified in 2 atrial septal defects with deviated curves. Conclusion : The environmental and effective factors on the heart development within embryonic evolution as well as the possibility of the existence of the mutation in coding genes of the other cardiac transcription factors such as GATA4 and TBX5 can be the reasons for the lack of the pathogenic mutation in this study. It is suggested in further related studies to investigate normal and abnormal cardiac tissue samples of these studied patients and coding genes of the other cardiac transcription factors.