The endothelial NO synthase (eNOS) enzyme is expressed during the early stages of cardiogenesis and plays an important role in normal heart development. Genetic variations of eNOS G894T have been shown to influence individual susceptibility to some phenotypes of congenital heart disease (CHD) in different populations. We conducted a case-control study comprised of 945 CHD patients and 972 non-CHD individuals in a Chinese population. Two functional single nucleotide polymorphisms (SNPs) (T-786C: rs2070744 and G894T: rs1799983) and one tagging SNP (rs7830) were evaluated in our study, and we assessed their association with the risk of CHD. Compared with the rs7830 CC/AC genotypes, the eNOS rs7830 AA genotype showed a significantly increased risk of CHD (adjusted odds radio (OR) = 1.45, 95% confidence interval (CI = 1.13-1.85). A stratified analysis was performed and showed that the association between the rs7830 AA genotype and CHD risk was stronger in patients with perimembranous ventricular septal defects (adjusted OR = 1.62, 95%CI = 1.20-2.20). Our results suggest that the eNOS rs7830 polymorphism may contribute to the susceptibility of sporadic CHD in a Chinese population.