The object of the study was to elucidate the mutations of the GATA4 gene in Han ancestry patients with congenital cardiac septal defects. Fifty Han ancestry patients with sporadic and familial cardiac septal defects and 200 normal subjects of the same ethnical background were studied. A total of six exons and the intron–exon boundaries of GATA4 were amplified by polymerase chain reaction (PCR). The PCR products were purified and directly sequenced with an ABI PRISM 3730 Automatic DNA sequencer. Two novel heterozygous mutations were discovered in the GATA4 gene in five children with cardiac septal defects (10%, 5/50), His28Tyr in exon 2 and His436Tyr in exon 7, respectively, which were neither found in the control population nor reported in the SNP database at the website http://​www.​ncbi.​nlm.​nih.​gov/​SNP. In addition, we did not identify any mutations in GATA4 in three familial atrial septal defects and two familial ventricular septal defects. Our finding suggests that the mutations in the transcription factor GATA4 might be related to congenital cardiac septal defects in Han ancestry patients.