To elucidate cytogenetic alterations underlying human hepatocellular carcinomas (HCCs), we used a comparative genomic hybridization (CGH) method to analyze 41 cases of hepatocellular carcinoma (HCC) including 15 well differentiated HCCs, 14 moderately differentiated HCCs, and 12 poorly differentiated HCCs. Of these, 27 patients were chronically infected with hepatitis C virus (HCV), and the remaining patients were positive for hepatitis B virus (HBV). The most common sites of increase in DNA copy number were 1q (78% of the cases) and 8q (66%) with minimal overlapping regions at 1q24-25 and 8q24, respectively. Frequent decreases in copy number were observed at 17p (51%), 16q (46%), 13q13-14 (37%), 4q13-22 (32%), 8p (29%), and 10q (17%). In 6 cases (15%), an amplification was found in the region of 11q13. A gain of 8q24 was significantly associated with well-differentiated HCCs (PF.05), whereas a loss of 13q13-14 and amplification of 11q13 were linked to moderately and poorly differentiated HCCs (PF.01). These observations suggest that a gain of 8q24 is an early event and that a loss of 13q13-14 and amplification of 11q13 are a late event in the course of liver carcinogenesis. A gain of 10q (7/41) was detected exclusively in cases with HCV infection. In contrast, an amplification of 11q13 was preferentially found in HBV-positive HCCs. These findings raise the hypothesis that, although many genetic alterations are basically common to both HCV-positive and HBV-positive tumors, the process of carcinogenesis may be to some extent different between these two types of tumors. (HEPATOLOGY 1999;29:1858-1862.) Hepatocellular carcinoma (HCC) is one of the most common human malignant tumors in the world. 1 It is widely accepted that hepatitis B (HBV) or C virus (HCV) infection, subsequent chronic inflammation and hepatocyte regeneration play important roles in the development of HCC. 2,3,4 However, the effects of viral infection on hepatocellular transformation remain to be determined. Accordingly, it remains unknown whether carcinogenetic process is different in HBV-positive and HCV-positive livers. HCC, like many other tumors, is considered to develop and progress as a consequence of an accumulation of genetic alterations. 5 Many investigators have made varying attempts to find genes implicated in hepatocarcinogenesis to construct a genetic pathway in the progression of HCC. 6,7,8,9 Although frequent allelic losses at loci of chromosomes 1p, 4q, 5p, 5q, 8p, 10p, 11q, 13q, 16q, and 17p have been reported in HCCs, 10,11 most of these studies failed to provide consistent information concerning genetic changes leading to the evolution of HCC. Comprehensive analysis is necessary to thoroughly understand the complicated genetic alterations in malignant tumors. Determination of these comprehensive genetic changes in solid tumors is practically difficult, because the examination of many individual genes by conventional methods is laborious and cumbersome. Screening for chromosomal regions with frequent gains and losses is one of t...