Background We retrieved different reports containing different genetic effects of A/B polymorphism within the Glutathione S-Transferase Mu 3 (GSTM3) intron 6 on the susceptibility to cancer in the overall population. Methods Herein, we first conducted a meta-analysis to comprehensively assess such a genetic relationship after collecting the available published evidence. STATA 12.0 software was used for the statistical analysis. Results By retrieving and screening database literature, a total of fifty-three eligible articles were finally selected. Even though no significant difference between overall cancer cases and negative controls was detected under the allelic, homozygotic, heterozygotic, dominant and recessive genetic model, we observed a reduced risk of head and neck cancer in cases, compared with controls, under the homozygotic model (BB vs. AA, P =0.047, OR=0.75) and recessive model (BB vs. AA+AB, P =0.045, OR=0.76), but not other models. Furthermore, a decreased risk of head and neck SCC cancer was detected under all the genetic models (allelic B vs. A, P =0.007, OR=0.78; BB vs. AA, P =0.006, OR=0.54; AB vs. AA, P =0.045, OR=0.82; AB+BB vs. AA, P =0.002, OR=0.77; BB vs. AA+AB, P =0.021, OR=0.63; carrier B vs. A, P =0.032, OR=0.83). Conclusion Our findings suggested that the GSTM3 intron 6 A/B polymorphism may confer the protective susceptibility to the squamous cell carcinoma of head and neck.