In this study, we first determined the promoter methylation pattern of seven individual genes, including P16, CCNA1, DCC, TIMP3, MGMT, DAPK, and MINT31, in 57 paired salivary rinses collected with or without an exfoliating brush from patients with HNSCC, and then evaluated the concordance of promoter hypermethylation between salivary rinses collected without brush and those with brush. Here, CCNA1 is linked to head and neck squamous cell carcinoma.