DNA-methyltransferase-3B (DNMT3B) may play an oncogenic role during tumorigenesis, and its genetic variants have been reportedly to be associated with risk of several cancers, but few studies have investigated their roles in squamous cell carcinoma of the head and neck cancer (SCCHN). Here we report a hospital-based case-control study with 832 SCCHN patients and 843 cancer-free controls of non-Hispanic whites that evaluated the association between two DNMT3B single nucleotide polymorphisms (SNPs) DNMT3B -149C>T (rs2424913) and DNMT3B -579G>T (rs2424909) in the promoter region and risk of SCCHN. We found that compared with C-allele carriers, the DNMT3B -149 TT genotype was statistically significantly associated with increased risk of SCCHN (adjusted OR, 1.35, 95% CI, 1.01-1.80, P=0.043), whereas the DNMT3B -579 TT genotype showed only a non-statistically significant risk compared with G-allele carriers. Further analysis of the effects of combined genotypes suggested that subjects with either DNMT3B -149 TT or DNMT3B -579 TT homozygous genotypes had statistically significantly increased risk of SCCHN (adjusted OR=1.36, 95% CI=1.07-1.73, P=0.013). Stratification analysis showed a more profound risk in the subgroups of the young (< or =57 years, the median age of the controls), males, current smokers, current drinkers, and patients with primary tumor sites of pharynx and larynx. This large study provides reliable risk estimates for associations between DNMT3B variants and SCCHN risk in non-Hispanic whites, and our findings are consistent with that of previously reported cancer case-control studies of other cancers. Further mechanistic studies are needed to unravel the underlying molecular mechanisms.