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. Here, CCNA1 is linked to neoplasm.