Epigenetic changes have been implicated in the pathogenesis of solid tumors, including head and neck squamous cell carcinoma (HNSCC). Prior efforts have primarily examined regional promoter hypermethylation as a silencer of tumor suppressor gene expression. To analyze the global state of methylation in the HNSCC genome, we utilize pyrosequencing of repetitive elements (LINEs) to compare the state of global methylation in HNSCC to normal aerodigestive mucosa. 137 samples (119 HNSCC tumors and 18 normal mucosal tissues) were digested to extract DNA and subjected to bisulfite treatment. Treated DNA was amplified using PCR primers for the repetitive LINEs sequence and produced a heterogeneous sample of products, from many genomic loci. These products were pyrosequenced to quantitatively evaluate their global genomic methylation status. HNSCC specimens showed global hypomethylation, with a mean level of genomic methylation of 46.8% methylated with a standard deviation of 9.0. Conversely, the normal upper airway mucosa had a global methylation level of 54.0 and a standard deviation of 4.6 (Mann-Whitney p value < 0.001). The tumor specimens also showed an increasing degree of hypomethylation associated with advanced tumor stage (ANOVA p-value of 0.003). About 67% of HNSCC's are globally hypomethylated when evaluated against the minimum level of methylation in the normal mucosal specimens. Degree of global hypomethylation was associated with smoking history, alcohol use and stage in univariate analysis (p-value 0.02), however, only HNSCC diagnosis remained significant on multivariate analysis. Despite the presence of regional promoter hypermethylation, HNSCC demonstrates global genomic hypomethylation. The effects of stage, alcohol use and smoking on global hypomethylation were not independently significant. ' 2007 Wiley-Liss, Inc.Key words: DNA hypomethylation; head and neck squamous cell carcinoma; pyrosequencing; epigenetics; smoking exposure; tobacco Head and neck squamous cell carcinomas (HNSCCs) account for 3% of all cancers in the United States and 40,000 new cases each year.1 Although significant progress has been made in the areas of early detection, diagnosis and treatment, the 5-year survival rate for patients with HNSCC has shown only modest improvement in the past 40 years.2 Comprehensive analysis of clinical and treatment factors has shown tumor-site specific improvements in 5-year survival for cancers of the nasopharynx, oropharynx and hypopharynx, and late-stage laryngeal cancer. The molecular mechanisms of HNSCC carcinogenesis are undergoing intensive investigation. Despite significant genetic/ epigenetic alterations found in these cancers, few known alterations correlate with the clinical outcomes of the disease. Epigenetic changes have been characterized in the pathogenesis of HNSCC. By far, the most studied epigenetic mechanism has been promoter hypermethylation of tumor suppressor genes including: Cyclin A1, MGMT, DCC and p16. 4 Methylation of cytosineguanine dinucleotides by the enzyme class of DN...