Cancers are based upon 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 these molecular events at each level. Microarray technologies have been extensively used to evaluate genetic alterations associated with cancer onset and progression in clinical oncology. The clinical impact of the genomic alterations identified by microarray technologies are growing rapidly and array analysis has been evolving into a diagnostic tool to better identify high-risk patients and predict patient outcomes from their genomic profiles. Here, we discuss the state-of-the-art microarray technologies and their applications in clinical oncology, and describe the potential benefits of these analysis in the clinical implications and biological insights of cancer biology.