Abstract: Objective To investigate the association between polymorphism of methylenetetrahydrofolate reductase gene (MTHFR) and the risk of congenital heart disease (CHD) and to provide references for CHD control.Methods A hospital-based case-control study was conducted in 2012 among 150 children with simple CHD and 150 healthy children vistiting the same hospital for physical examination.The genotypes of MTHFR C677T,A1298C,G1793A of the participants were determined with polymerase chain reaction and restriction fragment length polymorphism analysis (PCR-RFLP) and analyzed.Results Compared with the wild CC genotype,the heterozygosity (CT) of MTHFR C677T is associated with the increased risk of CHD (odds ratioOR=2.249,95%confidence interval95%CI:1.305-3.877,P=0.003) and the homozygous mutant genotype (TT) is associated with the increased risk of CHD significantly (OR=3.121,95%CI:1.612-6.043,P=0.001);compared with the wild allete (C),the mutant allete (T) of MTHFR C677T is associated increased risk of CHD (OR=1.813,95%CI:1.310-2.508,P=0.000).Compared with wild AA genotype,the heterozygosity (AC) of MTHFR A1298C is associated with the increased the risk of CHD (OR=2.177,95%CI:1.183-4.077;P=0.011) and the mutant allete (C) is associated with the increased risk of CHD (OR=2.017,95%CI:1.128-3.604;P=0.016).No statistical differences in the frequencies of the heterozygote (GA) and homozygote (AA) and the mutant and wild allete of MTHFR G1793A were observed between the cases and the controls (P=0.145,P=0.158).There are joint effects of MTHFR C677T and MTHFR A1298C,MTHFR A1298C and MTHFR G1793A on the risk of CHD.Conclusion These findings suggest that genetic polymorphism in MTHFR C677T and MTHFR A1298C might contribute to the risk of CHD incidence and there are interactions for the effects of MTHFR C677T and MTHFR A1298C,MTHFR A1298C and MTHFR G1793A.