Hepatocellular carcinoma is a highly malignant tumor that is prevalent in Southeast Asia and China, where hepatitis B viral infection is the main etiologic factor. Despite a high incidence of hepatocellular carcinoma developing in patients with viral hepatitis B-induced liver cirrhosis, the molecular events underlying the malignant liver progression remain largely unclear. In an effort to characterize the genetic abnormalities involved in the hepatitis B-related liver carcinogenesis, we performed genome-wide explorations by the technique of comparative genomic hybridization (CGH) on 100 hepatocellular carcinoma tumors that arose from hepatitis B-induced liver cirrhosis. According to the American Joint Committee on Cancer staging, four cases were classified as stage I, 69 as stage II, 23 as stage III and four as stage IV. CGH analysis indicated chromosomal instability in both early (stages I/II) and advanced (stages III/IV) stage tumors, with common gains on 1q, 8q and 17q23-q25, and losses on 4q22-q35, 8p21-p22, 13q14-q21, 16q and 17p identified in both groups (P40.05). Nevertheless, preferential sites of chromosomal defects in relation to hepatocellular carcinoma progression were also identified. Statistical correlations suggested a higher incidence of regional 1q21-q22, 3q22-q28, 7q21-q22 and 7q34-q36 over-representations in association with the advanced stage tumors (Po0.05). In this study, our novel identification of specific chromosomal aberrations in relation to the advanced stage tumors may represent a first step towards mapping genes linked to the progression of hepatocellular carcinoma. Modern Pathology (2005) 18, 686-692, advance online publication, 17 December 2004; doi:10.1038/modpathol.3800345 Keywords: hepatocellular carcinoma; hepatitis B virus; liver cirrhosis; progression Hepatocellular carcinoma is a primary liver malignancy that is highly malignant and rapidly fatal. The dismal clinical outcome is largely due to the majority of hepatocellular carcinoma tumors being asymptomatic during the natural course of the disease, consequently rendering most patients not being diagnosed in time for curative surgery. 1 By the time of clinical presentation, intra-and extrahepatic metastases are also common, which in turn has limited the scope of curative surgery. 2 In addition, the relatively high incidences of hepatocellular carcinoma recurrence, possibly from micrometastasis prior to surgical treatment, has further lowered the 5-year survival rate for individuals diagnosed with hepatocellular carcinoma. 3 The understanding of molecular events involved in the malignant liver progression thus would hold much value in the prognosis for patients with hepatocellular carcinoma.Studies on the molecular pathogenesis have guided the development of gene-based biomarkers in a number of human cancers including breast, colon, prostate and lung. 4 In hepatocellular carcinoma, although genetic characterizations have indicated frequent chromosomal over-representations on 1q, 6p, 8q, 17q and 20q, and deletions on 1p, 4q, ...