Tumors develop through the combined processes of genetic instability and selection, resulting in clonal expansion of cells that have accumulated the most advantageous set of genetic aberrations. Many types of instability may occur, resulting in point mutations, chromosomal rearrangements, DNA dosage abnormalities, and epigenetic changes such as methylation. In order to identify novel molecular targets for cancer therapy, we have focused on genomic copy-number aberrations as landmarks. Recent advances in array-based CGH technology (CGH-array) have enabled examination of chromosomal regions in unprecedented detail, prompting us to screen cancer-related genes including candidates of molecular targets. Indeed, applying our in-house CGH-array, we have identified several amplification target oncogenes as well as tumor suppressor genes. Useful molecular targets for cancer therapy will be identified more rapidly through exploring genomic and/or epigenomic abnormalities using genomic arrays including CGH-array system.