Our meta-analysis suggested that DNMT3B −149C/T polymorphism was associated with the risk of head and neck cancer under heterozygote comparison (OR 0.73, 95 % CI 0.59–0.90) and dominant model (OR 1.75, 95 % CI 0.62–0.92), although no evidence of association between DNMT3B −149C/T polymorphism and cancer risk was observed as we compared in the pooled analyses (homozygote comparison: OR 0.96, 95 % CI 0.86–1.09; heterozygote comparison: OR 1.07, 95 % CI 0.86–0.32; dominant model: OR 1.03, 95 % CI 0.85–1.25; recessive model: OR 0.93, 95 % CI 0.8–1.08). The gene discussed is DNMT3B; the disease is cancer.