This study aims to evaluate the influence of methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms on congenital heart diseases (CHD) risk. The frequencies of allelic and genotypic in CHD patients were significantly different from non-CHD controls. Our data suggested that the c.1333C > T genetic polymorphism of MTHFR gene was statistically associated with the increased risk of CHD [TT versus CC: odds ratio (OR) = 2.70, 95% confidence interval (CI) 1.34-5.45, p = 0.005; T versus C: OR = 1.38, 95% CI 1.03-1.86, p = 0.032]. Our findings indicate that the c.1333C > T genetic polymorphism influences CHD risk in the studied population.