The sequentiation of the human genome, together with the development of high throughput technologies, particularly gene-expression profiling, is giving us the opportunity to describe biological features in a quantitative manner. Here we review the use of global gene expression analyses in cancer research. Microarray analyses of tumor samples have allowed researchers the development of profiles that can distinguish, identify and classify discrete subsets of disease, predict the disease outcome, or the response to therapy. Profiling of experimental models with activation of certain oncogenic pathways could also be used to ascertain the molecular events involved in the establishment and development of tumors and, consequently, these models could be validated as tools for preclinical therapy. Furthermore, the detailed analysis of gene expression deregulation after response to the therapies in such models would allow us to predict the response to specific drugs, and to target the therapies to patients in search for individualized management of the disease.