The nuclear factor of activated T lymphocytes (NFATc1) plays a critical role during valvular and septal development. Genetic variants may influence the biological function of the protein and thus play a role in susceptibility to valvuloseptal defects. Tandem repeat polymorphisms and a common nonsynonymous polymorphism (Cys751Gly) of NFATc1 were genotyped in a hospital-based case-control study of 241 patients with valvuloseptal cardiac defects and 557 controls. The risk of valvuloseptal defect associated with the variant homozygote (LL) was significantly greater than that of the wild-type homozygote. Based on stratification analyses by congenital heart disease types, individuals with the LL genotype were postulated to have a higher risk of perimembranous ventricular septal defect (adjusted OR = 1.68, 95% CI = 1.02-2.78). These findings suggest the usefulness of the NFATc1 tandem repeat polymorphism as a biomarker of perimembranous ventricular septal defect susceptibility.