With the control sample type, a significant association between DAPK promoter methylation and HNSCC was found among the tissue group and the non-tissue group in the random-effect model (tissue group, OR = 3.95, 95% CI = 1.89–8.25; non-tissue group, OR = 5.30, 95% CI = 2.17–12.93). This evidence concerns the gene DAPK1 and head and neck squamous cell carcinoma.