The HOXA1 gene plays a fundamental role in embryonic morphogenesis. Recent studies in humans and mice have indicated that HOXA1 plays a previously unrecognized role in cardiovascular system development. Congenital heart disease (CHD), particularly ventricular septal defect (VSD), might be a clinically isolated manifestation of HOXA1 mutations. The purpose of the present study was to identify potential pathological mutations in the HOXA1 gene in Chinese children with VSD and to gain insight into the etiology of CHD. A total of 340 nonsyndromic VSD patients and 200 normal subjects were sampled. Two exons and the nearby introns of the human HOXA1 gene were amplified using polymerase chain reaction (PCR). The PCR products were purified and directly sequenced. However, no nonsynonymous mutations in the coding regions of the HOXA1 gene were observed: Only two novel synonymous mutations (c.C210T p.His70His, and c.T861A p.Arg287Arg) were found in two patients. Two previously reported single and multiple histidine-deletion variants were identified in both normal and VSD patients. To our knowledge, this is the first study to investigate the role of the HOXA1 gene in CHD. Although our results did not show any pathogenic HOXA1 mutation, our results suggest that VSD might not be a clinically isolated manifestation of HOXA1 mutations.