Despite animal studies having demonstrated that Tbx20 is essential for heart development, few studies have been conducted about TBX20 and congenital heart disease (CHD) in humans. Recently two TBX20 mutations have been associated with human heart defects in two Caucasian families, but TBX20 mutations underlying the more common isolated forms of CHD are still unknown. To explore this question and to analyze the association between TBX20 and susceptibility to CHD 203 Chinese patients with a variety of predominantly sporadic CHD and 300 control subjects were investigated for TBX20 mutations. The exon 2-6 contributing to the T-box DNA-binding domain and their flanking intron sequences were amplified by polymerase chain reaction (PCR) and then were sequenced after purification. Three non-synonymous mutations (A63T, I121F, and T262M) were identified in 3 patients, which were not seen in 300 controls. I121F and T262M mutations occurred within the highly conserved T-box DNA-binding domain. Two synonymous sequence variants (N222N, T262T) and one intervening variant (IVS2-5insCT) were observed in 3 patients but not in the controls. In addition, eight SNPs were observed both in patients and controls and four (S167S, P177P, A181A, and I219I) of them are novel. These data indicate that the frequency of TBX20 missense mutations occurred in Chinese CHD children is low, but they probably contribute to the risk of atrial septal defect (ASD), total anomalous pulmonary venous connection (TAPVC) and tetralogy of Fallot (TOF) in a small subset of Chinese. The findings provide the first insight into TBX20 mutations for TOF and TAPVC. Functional study involved in the new sequence variants should be subject of further investigation.