Cancer development and progression is a complex process that involves a host of functional and genetic abnormalities. Genomic perturbations and the gene expression they lead to, can now be globally identified with the use of DNA microarray. This relatively new technology has forever changed the scale of biological investigation. The enormous amount of data generated via a single chip has led to major global studies of the cellular processes underlying malignant transformation and progression. The multiplicity of platforms from different proprietors has offered investigators flexibility in their experimental design. Additionally, there are several more recent microarrays whose designs were inspired by the nucleotide-based technology. These include protein, multi-tissue, cell, and interference RNA microarrays. Combinations of microarray and other contemporary scientific methods, such as, laser capture microdissection (LCM), comparative genomic hybridization (CGH), single nude-otide polymorphism analysis (SNP) and chromatin immunoprecipitation (ChIP), have created entirely new fields of interest in the more global quest to better define the molecular basis of malignancy. In addition to basic science applications, many clinical inquiries have been performed. These queries have shown microarray to have clinical utility in cancer diagnosis, risk stratification, and patient management.