Congenital heart defects are complicated birth defects due to the interaction of genetic and environmental factors. Previous research indicated the importance of transcription factors in heart development, which suggested that mutations of transcription factor genes could be genetic determinants of congenital heart defects. Recently, the length variation of an intronic region in the NFATC1 gene was linked to ventricular septal defect (VSD). In this study, we detected the length variation of the region in a Han Chinese population of patients with nonsyndromic VSD, atrial septal defect, patent ductus arteriosus, and control individuals. We found a new allele of the length variation with four repeats of a 44-bp region. At the same time, all the alleles were found in both patient and control groups and there were no significant differences in genotype distribution between the patients and controls. The results suggested no association of the length variation of the intronic region in NFATC1 gene with VSD, atrial septal defect, and patent ductus arteriosus.