De novo DNA methylation is a relevant epigenetic mechanism, which represses gene transcription and commonly inactivates tumor suppressor genes in carcinogenesis. A single nucleotide polymorphism of DNMT3B, C46359T (-149C-->T) was reported to modulate individual's susceptibility to cancer. We investigated the role of this polymorphic variant regarding the methylation status of the p16CDKN2A gene in young and older patients with head and neck squamous cell carcinoma (HNCC) matched by the TNM staging system, together with its impact on patients survival. The results showed that the presence of the allele T of the polymorphism DNMT3B (-149C-->T) was associated with advanced TNM staging and smoking habit, but no association was found between this polymorphisms and DNMT3B immunostaining. While p16CDKN2A methylation was significantly associated with smoking habit in older patients, this parameter was associated with family history of cancer in young patients. Moreover, in older patients the absence of p16CDKN2A promoter methylation had a negative impact on survival. In conclusion, nucleotide polymorphism of DNMT3B is not associated with methylation of p16CDKN2A gene in HNSCC. The association of p16CDKN2A gene methylation with smoking, family history of cancer and survival is dependent on age.