Purpose: The aim of this study was to investigate the prognostic value of hypermethylation of tumor suppressor genes in patients with non-small cell lung cancer (NSCLC). Experimental Design: We examined the methylation status of nine genes in 155 tumors from patients with NSCLC using quantitative methylation-specific PCR. We analyzed the associations between gene methylation status and overall patient survival. Results: The methylation index, defined as the ratio between the number of methylated genes and the number of genes tested, was significantly higher in adenocarcinomas (0.38 F 0.20) than in squamous cell carcinomas (0.30 F 0.22; P = 0.027), in tumors from older patients (0.37 F 0.20) than younger patients (0.30 F 0.22; P = 0.040), and in tumors from heavier smokers (0.39 F 0.21) than lighter smokers (0.29 F 0.20; P = 0.042). In the Cox proportional hazards model, p16 methylation was associated with significantly poorer survival [hazard ratio, 1.95; 95% confidence interval (95% CI), 1.21-3.39]. Kaplan-Meier survival curves showed that patients with hypermethylated p16 had significantly shorter survival (median = 21.7 months) than patients without p16 hypermethylation (median = 62.5 months; P = 0.0001, log-rank test). Hypermethylation of CDH1 orTIMP3 gene was associated with significantly better survival with hazard ratios of 0.51 (95% CI, 0.29-0.90) and 0.59 (95% CI, 0.36-0.97), respectively. Joint analysis of these three genes showed a significant trend for poorer survival as the number of unfavorable events increased (P = 0.0007). Conclusion: Hypermethylation of multiple genes exhibited significant differential effect on NSCLC patient survival. Assessment of the effect of each methylated gene on survival is needed to provide optimal prognostic value.Both in the United States and around the world, lung cancer is the leading cause of cancer death in men and women, with a 5-year survival rate of only 15%, a statistic that has changed very little over the past two decades (1). This dismal survival could be improved through earlier detection or through identification of prognostic markers, which could identify subsets of patients with worse prognosis who might benefit from a more aggressive treatment strategy.It is now well established that epigenetic changes (i.e., heritable changes in gene expression without alterations in the primary DNA sequence of a gene; refs. 2, 3) play an important role in cancer development. The major epigenetic aberration in cancer development is inactivation of tumor suppressor genes (TSG) through hypermethylation of CpG islands in their promoter regions. The spectra and frequency of TSG inactivation at the CpG islands vary from cancer to cancer (3 -5). The distinct profile and varying levels of TSG methylations among different cancers, coupled with a sensitive methylation-specific PCR (MSP) technique, have shown promise as a tool for the early detection and diagnosis of cancer and for determining prognosis (5 -9).A number of genes are heavily methylated in non -small cell...