In this study, we describe a five DNA methylation panel (RASSF1α, p16INK4a, TIMP3, PCQAP 5′ and PCQAP 3′) that can discriminate HPV-negative and HPV-positive HNSCC patients from normal healthy control smokers and non-smokers. Here, CDKN2A is linked to head and neck squamous cell carcinoma.