Background Congenital heart disease (CHD) is a diverse group of diseases determined by genetic and environmental factors. Considerable research has been done on genes associated with the development of the heart. Recently, focus is on the role of transcription factor NFATc1 in the development of proper valve and septa. As part of a larger study, high density single nucleotide polymorphism (SNP) scanning was used to explore the relationship between NFATc1 gene polymorphism and susceptibility to ventricular septal defect (VSD) in the Chinese Han population. Methods One hundred and ninety-two pediatric patients with congenital VSD and 192 matching healthy control subjects were studied. The haplotype reconstructions were calculated by PHASE2.0 software. Haploview software was used to perform linkage disequilibrium assessment and define haplotype blocks. The algorithm used for defining the blocks was the confidence interval method. Results The NFATc1 gene region can be divided into 11 haplotype blocks. Strong linkage disequilibrium existed within blocks 6, 8, 9, and 11. Three SNPs (rs7240256, rs11665469, and rs754505) within the NFATc1 gene had significant correlation with VSD by single marker association analysis. In addition, two haplotypes correlated with VSD. Conclusions NFATc1 is associated with the occurrence of VSD and it may be a predisposing gene to CHD in Han Chinese. This finding has set a direction for further genetic and functional studies.