Congenital heart disease (CHD) is a common congenital birth defect, affecting nearly 1% of all live births, and is the most common cause of infant death. NKX2.5 is an important transcription factor expressed during vertebrate heart development and involved in the regulation of septation during cardiac morphogenesis and in the maturation and maintenance of the atrioventricular node throughout life. There are many reports on association of single-nucleotide polymorphisms (SNPs) of NKX2.5 with CHD but none have been reported from Mysore, South India. With informed consent, 150 clinically diagnosed CHD patients and 70 unrelated healthy controls in Mysore, South India, were recruited. In the first phase the DNAs of 50 CHD patients and 20 controls were subjected to polymerase chain reaction amplification of coding regions of NKX2.5 and further sequenced for SNP genotyping. Additionally, mass array analysis of SNPs was performed for 100 CHD and 50 controls. Analysis revealed the occurrence of six SNPs in different types of CHDs. Two were synonymous SNPs, the most common c.239A>G (p.E21E) and newly identified c.896C>A (p.A240A), as well as three nonsynonymous SNPs, c.608A>G (p.E203G), c.646C>T (p.R216C), and c.852G>A (p.N226D). The sixth SNP 1212G>T in the 3'UTR was observed in 40% of the CHD cases. The SNPs c.646C>T and c.608A>G were shown to cause changes in their secondary structure. Ventricular septal defect was the more prominent CHD observed in our study population. The SNPs c.608A>G (p.E203G) and c.852G>A (p.N226D) were present only in CHD patients, indicating their association with CHDs.