Abstract: Objective To investigate the risk factors of birth defects in children under 5 years of age in Jilin Province, and to provide scientific basis for formulating comprehensive prevention and control strategies for birth defects. Methods Birth defects in the sample survey of children under 5 years of age in Jilin Province were treated as case proup. Normal children were drawn at equal proportion as control group. A case-control study was conducted with 379 cases and 379 controls. Data was analyzed for descriptive study. Univariate Logistic regression and multivariate Logistic regression were analyzed with SPSS 21.0 software. Results Multivariate Logistic regression analysis showed that mother's occupation was worker(OR=4.328, 95% CI:1.416-13.227, P=0.010)and houseworker(OR=2.602, 95% CI:1.311-5.163, P=0.006), mother was sick before and during pregnancy (OR=4.074, 95% CI:1.413-11.746, P=0.009), mother had a bad pregnancy outcome before the defect child (OR=2.640, 95% CI:1.696-4.110, P<0.001), mother had a fever(>38℃) in the early weeks of pregnancy(OR=8.924, 95% CI:2.856-27.889, P<0.001)were risk factors of birth defects. Mother took low dose of folic acid supplements before pregnancy, and prenatal down syndrome screening were protective factors (all P<0.05). Conclusions Preconception and early pregnancy intervention, avoiding risk factors and supplementation of folic acid are important to prevent birth defects.