The sequencing of the human genome has formed the foundation with which to develop technologies and reagents to perform true genome-scale biological studies. In particular, the development and increasing application of these high-throughput genome-scale technologies have fundamentally altered the way one can approach the analysis of cancer. It is now possible to imagine studies that interrogate the structure, expression and function of every gene in a comprehensive, highly parallel fashion, permitting the development of multidimensional, global views of cancer. In this review, we focus on recent advances in the application of genomic strategies to the study of cancer, with an emphasis on functional genomics and the prospects for integrating the knowledge gained from these approaches to further develop our understanding of cancer and design better therapeutic strategies.