Objective　To identify mutations of GATA4 and GATA6 genes in children with isolated congenital atrial septal defect (ASD). Methods  From November 2012 to November 2013, 101 patients with ASD (99 unrelated patients and one twin) who were submitted to catheter-based intervention and 100 ethnicity-matched children without congenital heart disease, blood disorders and chromosomal abnormalities were enrolled. The blood was collected. The coding regions and flanking regions of the GATA4 and GATA6 genes were amplified by polymerase chain reaction and sequenced using the dideoxvnucleotide chain termination technique, and then compared with the normal sequence in the Genbank. Results  Two novel heterozygous missense GATA6 mutations, c. G145A and c. G151A, were identified in 2 unrelated ASD patients, which were not present in the controls. These two mutations predicted the conversion of glycine into serine at amino acid residue 49 (G49S) and glutamate into lysine at amino acid residue 52 (K52E). A heterozygous missense GATA6 mutation c.43 G>C, which caused a conversion from glycine to arginine, was found in 9 ASD patients and 7 controls. A single nucleotide polymorphism c.99G>T, which did not cause amino acid conversion in GATA4 gene, was found.  Conclusions  GATA6 gene is an important transcription factor in heart development. The mutation of GATA6 gene may cause the change of its transcriptional activity, and lead to ASD.