Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Long-term survival of this patient group has been marginally improved during the last 30 years. This is due to the high recurrence rate of local primary or development of second primary tumours in the patients. We found that normal-appearing surgical margins and distant mucosal tissue of HNSCC patients contained tumour suppressor genes DNA methylation. These cells might be the progenitors of the tumour recurrences. Such molecular abnormalities in the normal-appearing mucosa tissue were not possible to detect in the clinic or by standard histopathologically analysis. To improve clinical outcome, the convenient and cost-effective molecular analysis such as methylation-specific PCR should be added to the pathological diagnosis armamentarium for HNSCC patients. The beneficial effect of antimethylating agents as additional treatment or for cancer chemoprevention, in this high-risk patient group, warrants further investigation.