To elucidate the birth defects of children in women received In Vitro Fertilization-Embryo Transfer (IVF-ET) by conducting a meta-analysis. We conducted a systematic literature search to identify original studies of birth defects in IVF-ET before Feb 2016. Eligible studies were retrieved via both computer searches and manual review of references. The summary difference estimates between groups were calculated based on the Weighted Mean Difference (WMD) with its 95% Confidence Interval (CI). Sensitivity and publication analyses were performed after the pooled analysis. A total of 15 original studies of 189376 new born were included in this study. Meta-analysis showed an increased level of birth defects rate in women received IVF-ET (Z=8.67, P<0.01). There was no significant publication bias in the included studies (P for Begg’s test=0.86, P for egger’s test=0.16). Congenital malformation in IVF-ET group was significantly higher than that in the control group (P<0.05) and the level of OR was 1.29 (95% CI, 1.20, 1.41). Our results demonstrated that there was an increased level of birth defects rate in women received IVF-ET.