Here, in this study, we analyzed the aberrant promoter methylation profile of HNSCC using seven important tumor-related pathway genes (p16, DAPK, GSTP1, ECAD, RASSF1, MLH1 and BRCA1) and three methylated loci (MINT1, MINT2 and MINT31) in the high cancer incidence zone of Northeast India. Here, CDH1 is linked to head and neck squamous cell carcinoma.