Our previous genome-wide association study (GWAS) identified two susceptibility loci for congenital heart disease (CHD) in Han Chinese. Here we identify additional loci by testing promising associations in an extended 3-stage validation consisting of 6,053 CHD cases and 7,410 controls. We find GW significant (P<5.0 × 10−8) evidence of 4 additional CHD susceptibility loci at 4q31.22 (rs1400558, upstream of EDNRA, Pall=1.63 × 10−9), 9p24.2 (rs7863990, close to SMARCA2, Pall=3.71 × 10−14), 12q24.13 (rs2433752, upstream of TBX3 and TBX5, Pall=1.04 × 10−10) and 20q12 (rs490514, in PTPRT, Pall=1.20 × 10−13). Moreover, the data from previous European GWAS supports that rs490514 is associated with the risk of CHD (P=3.40 × 10−3). These results enhance our understanding of CHD susceptibility.