Recurrent structural alterations, such as amplification, deletion, or translocation, are hallmark features of the cancer genome. Mapping of these DNA copy number aberrations, using approaches such as comparative genomic hybridization (CGH), has enabled the discovery of bona fide tumor suppressor genes and oncogenes. With the emergence of high-density oligo-based microarray platforms, array-based CGH has become a powerful technology that can facilitate the accurate mapping and rapid identification of novel cancer genes. Here, we describe the optimized technical protocol for comparative genomic hybridization with full-complexity genomic DNA on 60-mer oligonucleotide microarrays.