In the following study, we used comparative genomic hybridization (CGH) to screen and compare for genetic alterations of hepatocellular carcinoma (HCC) and intrahepatic choalgiocarcinoma (ICC). The studies showed distinctive features of genetic alterations between the two tumors. Characteristic abnormal changes for HCC were 1q gain and loss of 4q, 10q and 13q regions. In contrast, gains of 5p, 7p, 13q and 20q were more predominant in ICC. Losses of 16q, 17p, and 18q, and gain of 8q region showed a similar high frequency of incidence in both tumors. The most striking and different findings were 1q amplification in HCC and 20q gain in ICC. Our data indicate that ICC shows the pattern of genetic alterations similar to pancreatic and colorectal cancers. This suggests that the genetic alterations in tumorigenesis show a similar pattern depending on the origin of cells, not the organ.