Cancers are associated with an array of orchestrated genetic changes and the identification of changes causally related to the carcinogenic process. To elucidate the mechanism of cancer carcinogenesis, it is necessary to reconstruct molecular events at each level. Microarray technology is a versatile platform that allows rapid genetic analysis to take place on a genome-wide scale and has revolutionized to evaluate genetic markers and changes in cancer genetics. Since, their development in the mid-1990s, these technologies have become a key tool in the fight against cancer. Microarray data have led to the identification of molecular subclasses of solid tumors characterized by distinct oncogenic pathways, as well as the development of multigene prognostic or predictive models equivalent or superior to those of established clinical parameters. Currently, several genomic aberrations discovered by these assays are presently being used as predictive markers for cancer treatment with targeted therapeutics. But how do microarrays work and just how have they been used in cancer diagnosis and treatment thus far? Here, we presented a summary of the main applications of microarrays in the field of targeted therapies of cancer and discussed their potential in clinical implementation.