DNA hypermethylation in CCNA1, DAPK, DCC, MGMT, and TIMP3 is strictly correlated to the presence of OSCC tumor. Moreover, 100% of HNSCC patients with TIMP3 DNA hypermethylation, 6 months after treatment, had lower local recurrence-free survival. DNA hypermethylation on CCNA1, DAPK, DCC, MGMT, and TIMP3 genes is a specific OSCC diagnostic biomarker; TIMP3 DNA hypermethylation is an independent prognostic factor to recognize HNSCC patient subgroups with high risk of local recurrence. This evidence concerns the gene CCNA1 and head and neck squamous cell carcinoma.