Objective To systematically review the association between prenatal exposure to dichlorodiphenyltrichloroethane (DDT) or polychlorinated biphenyls (PCBs) and the risk of congenital anomalies. Methods PubMed, EMbase, WanFang Data, VIP and CNKI databases were electronically searched to collect case-control studies on the relationship between prenatal exposure to DDT or PCBs and congenital anomalies from inception to February 2017. Two reviewers independently screened literature, extracted data and assessed the risk of bias of included studies, then, meta-analysis was performed by using Stata 13.0 software. Results A total of 14 studies involving 2 238 infants with defect and 2 335 infants without defect were included. The results of meta-analysis showed that: the prenatal exposure to high level of DDT increased the incidence of cryptorchidism (OR=1.12, 95% CI 1.09 to 1.15, P<0.001). However, DDT exposure had no correlation to hypospadias and neural tube defects. The associations between prenatal exposure to PCBs and cryptorchidism, hypospadias, neural tube defects were not discovered. Conclusion Prenatal exposure to high levels of DDT may be a risk factor for cryptorchidism. Due to limited quality and quantity of the included studies, more high-quality studies are needed to verify above conclusion.