Objective To evaluate associations betweenMTHFD1 gene G1958A polymorphism and the risk of neural tube defects (NTDs). Methods We electronically searched databases including PubMed, The Cochrane Library, Web of Science, CNKI, VIP, and WanFang Data from inception to June 2016 to collect case-control studies of the correlation between the G1958A polymorphism inMTHFD1 and the risk of NTDs. Two reviewers independently screened the studies, extracted data and assessed the risk of bias of included studies, and then, meta-analysis was performed using Stata 12.0 software. Results Thirteen case-control studies were included, involving 1 724 NTDs infants, 1 485 mothers and 774 fathers with NTDs offspring. The results of meta-analysis showed that there was significant association betweenMTHFD1 gene G1958A polymorphism and increased risk of NTDs in infants (AAvs. GG: OR=1.437, 95%CI 1.100 to 1.878,P=0.008; AA+AGvs. GG: OR=1.187, 95%CI 1.031 to 1.367,P=0.017; Avs. G: OR=1.210, 95%CI 1.050 to 1.394,P=0.008). However, there was no association between biparentalMTHFD1 gene G1958A polymorphism and NTDs in the offspring. Conclusion The current evidence shows thatMTHFD1 gene G1958A polymorphism may be a genetic risk factor for NTDs. Due to the limited quantity and quality of the included studies, more high quality studies are needed to verify the above conclusion.