Microarray-based Comparative Genomic Hybridization (array-CGH) has been applied for a decade to screen for submicroscopic DNA gains and losses in tumor and constitutional DNA samples. This method has become increasingly flexible with the integration of new biological resources generated by genome sequencing projects. In this chapter, we describe alternative strategies for whole genome screening and high resolution breakpoint mapping of copy number changes by array-CGH, as well as tools available for accurate analysis of array-CGH experiments. Although most methods listed here have been designed for microarrays composed of large-insert clones, they can be adapted easily to other types of microarray platforms, such as those constructed from printed or synthesized oligonucleotides.