Hepatocellular carcinoma (HCC) etiology is genetically heterogeneous; multiple different mechanisms have been shown to promote hepatocarcinogenesis. However, chromosomal aberrations (CAs) and signaling pathways that they alter are still poorly understood. Changes in chromosome number (aneuploidies) or structural chromosomal aberrations, such as; amplifications, deletions, loss of heterozygosity and recessive mutations are important mechanisms for tumor evolution. Recently developed single nucleotide polymorphism (SNP) microarrays provide highthroughput quantitative and qualitative screening of genomic DNA with higher resolution compared to conventional methods such as fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH). In cancer research, SNP arrays ease the screening of structural changes as well as aneuploidies with exact physical position. In the framework of this study, we aimed to detect DNA copy number alterations in a panel of 14 HCC cell lines. We screened all the autosomal chromosomes and the Xchromosome and found previously undescribed novel regions that harbor homozygous and hemizygous deletions at 13q12 and Xq21; amplifications at 8p23, 8q13, 8q24, 9p22- 21, 12p1, 14q12, 15q21, 16q23, 17p12-p11, 17q11, 22q11 and Xp22. In our knowledge, our results are the first comprehensive high-throughput screen of commonly used HCC cell lines.