Genome-wide copy number detection using microarray technologies has been one of the recent topics in cancer genetics and also in the research on large-scale variations in human genomes. This chapter describes methods to analyze copy number alterations in cancer genomes using Affymetrix GeneChip, high-density oligonucleotide microarrays originally developed for large-scale single nucleotide polymorphism (SNP) typing. Combined with the large numbers of SNP-specific probes, the robust algorithms developed for analyzing raw array signals (Copy Number Analyzer for Affymetrix GeneChip v2.0) enable not only accurate and high resolution copy number estimations, but also allelic imbalances commonly found in cancer genomes, which provides a powerful platform to explore the complexities of cancer genomes.