Congenital heart disease (CHD) is one of most common birth defects threatening newborns' health. Over the past few decades, a variety of CHD-causing gene mutations have been identified, but the pathogenic mechanism of congenital heart disease is yet not very clear. The aim of this study was to identify potential pathologic mutations in the NODAL gene and to gain insight into the etiology of CHD. By using amplification with polymerase chain reaction and sequence analysis of NODAL in 800 patients with nonsyndromic CHD and 250 healthy controls, we identified 3 nonsynonymous variants. One of them was first identified in the present study. These variants were not observed in 250 controls. To our knowledge, this is the first study to suggest that NODAL may be involved in the etiology of nonsyndromic CHD in a Chinese population.