Atrial septal defect (ASD) is a developmental defect of the heart which arises from the congenital abnormality of interatrial septum that perturbs the normal blood flow. Development of the heart is a complex biological process regulated by numerous genetic and environmental factors. During this process DNA binding proteins Myocardin, NKX2.5 (NK2 Transcription Factor Related Locus-5) and GATA4 (GATA Binding Protein-4) function by binding to SRF (Serum Response Factor) which is also a key regulator of myogenic terminal differentiation and frequently results in mitogenesis. Several studies suggest that mutations in the homeodomain containing transcription factor, NKX2.5, is implicated with atrial septal defect. This cross sectional descriptive study was done to investigate the frequency of NKX2.5 gene mutations among the patient with ASD who were undergoing surgical repair at the National Institute of Cardiovascular Diseases (NICVD) and National Heart Foundation and Research Institute (NHF&RI), Dhaka from July 2010 to June 2011. Patients presented with ASD at any age of both sexes were selected as study population. We found six distinct polymorphic sites among Bangladeshi population. Among six polymorphic sites, two were located at position 487 and 495. These were present in around 80% of the affected individuals. However they were not present in control population. Our study also revealed that mutations present in the downstream sites or towards the end of the genes are restricted to older people, whereas mutations present towards the 5' site is common to population of all ages. This interesting relationship has encouraged us to raise two new hypotheses.