Primary hepatocellular carcinomas (HCCs) of different etiologies were studied to determine the rate of alteration of several genetic regions previously associated with the HCC phenotype. The focus of our study was to identify the frequency of genetic alterations within individual HCCs and their distribution among male and female cases. Genetic differences were evaluated between DNA isolated from tumor (T) and corresponding non-tumor (N) tissue using short tandem repeat (STR)-microsatellites and restriction fragment length polymorphism (RFLP) analyses. Twenty-eight HCC cases were studied with polymorphic markers from different parts of the genome. Three or more loci were identified with genetic alterations from 28 loci tested in 63% of HCC cases. Human hepatocellular carcinoma (HCC) remains a leading cause of cancer death worldwide. HCC has a very poor prognosis, and there is only limited understanding of the molecular events that lead to uncontrolled proliferation of the liver parenchymal cells. Several etiologic factors have been identified as high risk factors in association with HCC development, including previous infection with hepatitis B virus (HBV), hepatitis C virus (HCV), exposure to aflatoxin, and alcohol-induced cirrhosis. 1-4 However, it remains unclear how these agents affect hepatocyte growth, the transformation process, or both.Current research has focused on identifying the genetic region(s) in which a mutation leads to transformation in the hepatocyte and malignant proliferation in the liver because neoplasia is thought to result from the initiation and accumulation of genetic mutations in a multistep process. Genetic evolution of the tumor phenotype is best defined in colorectal cancer in which several sequential mutations have been identified in association with the stage of the disease. 5,6 Alterations of several chromosomal regions have been identified in HCC. 7-38 Some data suggest that certain HCC causes are associated with specific genetic alterations. 25,26,36 p53 is the only gene in which specific mutations have been associated with HCC, but even these mutations are recognized as later alterations in HCC development. [26][27][28][29] Epidemiological studies document the higher incidence of HCC among men than women but so far no correlation with genetic data was implicated. A recent study in 120 HCCs documented frequent loss of heterozygosity (LOH) in chromosome regions 1p, 1q, 2q, 4q, 6q, 8p, 9q, 16p, 16q, and 17p. 34 Despite a long list of loci with frequent LOH in HCCs the sequence of these mutations in HCC development is not understood.We and others have identified a high incidence of genetic alteration in the short arm of chromosome 1 in HCCs of different causes. [30][31][32][33] We now report that the majority of our HCC cases have multiple genetic alterations. The most frequent target for genetic change in HCCs analyzed is the 1p36 region. The frequent LOH in 1p36.1, 1p36.3, 4q28, 13q14, and 17p13 indicates important HCC suppressors in the vicinity of these regions. The 4q28 locus...