Background Genes of different pathways regulate spermatogenesis, and the complexity of the spermatogenic process indicates that polymorphisms or mutations in these genes could cause male infertility. Published data on the association between the GSTM1 and GSTT1 polymorphism and male infertility risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was performed. Methods A total of 11 studies regarding GSTM1 and 9 studies regarding GSTT1 between 1999 and 2012 were identified through researching MEDLINE, EMBASE and the Chinese Biomedical Database. It was performed to obtain summary estimated odd ratios and 95 % confidence intervals of GSTM1 and GSTT1 for male infertility, with attention to study quality and publication bias. Results Overall, a significant association was seen between GSTM1 (OR01.20, 95 % CI 01.02-1.40, P heterogeneity 0 0.000, P00.027) genotypes and male infertility. Significant associations were also observed in subgroups of Caucasian populations (OR01.65, 95 %CI01.16-2.34, P heterogeneity 0 0.006, P00.005), but were not observed in Asian populations (OR01.09, 95 % CI00.72-1.65, P heterogeneity 00.054, P00.697) when stratified by ethnicity. While there was no significant association was seen between GSTT1 (OR0 1.00, 95 % CI00.74-1.35, P heterogeneity 00.000, P00.980) null genotypes and male infertility. Simultaneously, significant associations were not observed in subgroups of Caucasian populations (OR 00.94, 95 %CI 00.44-2.00, P heterogeneity 00.000, P 00.867) and Asian populations (OR00.93, 95 % CI00.46-1.87, P heterogeneity 00.002, P0 0.838) when stratified by ethnicity. Conclusion Our results suggest the GSTM1 null genotype contributes to male infertility susceptibility, while GSTT1 gene polymorphisms are not associated with male infertility in our study.