ABSTRACTBackground: HCV infection is related to aberrant methylation of several genes. RASSF1A, E-Cadherinand RUNX3are tumour suppressor genes that may be inactivated by hypermethylation in many tumours including hepatocellular carcinoma (HCC). We hypothesized that methylation is a diagnostic biomarker for HCC in patients with HCV-related liver cirrhosis.Methods: We recruited 207 cases of HCV-related liver cirrhosis, 193 HCC patients and 53 healthy controls. Methylation-specific polymerase chain reaction for detection of circulating hypermethylated RASSF1A, E-Cadherinand RUNX3. Alpha fetoprotein (AFP) was measured by commercial immunoassay.Results: Significant hypermethylation of the three genes was found in the HCC group compared to both cirrhosis and healthy groups (P< 0.001), whereas no significant difference in hypermethylation was found between cirrhosis and healthy groups (P= 0.17, 0.50 and 0.14, respectively). No significant links were found between hypermethylated RASSF1A, E-Cadherinand RUNX3and stages of Barcelona Clinic of Liver Cancer score (P =0.21, 0.63 and 0.98, respectively). No significant associations were found between AFP value and hypermethylated genes in cirrhosis and HCC groups (P= 0.82) except with E-Cadherinin HCC (P= 0.02). In multiple regression analysis, RASSF1Aand E-Cadherinwere predictors of HCC within cirrhosis cases, but only E-Cadherinwas an independent risk factor for prediction of HCC in cases with low AFP (P= 0.01).Conclusions: The presence of hypermethylated serum RASSF1A, E-Cadherinand RUNX3is linked to HCC in patients with HCV-related cirrhosis. Only E-Cadherinis an independent risk factor for prediction of HCC with low AFP. These findings may be of diagnostic value.