Advances in our knowledge of the molecular basis of prostate cancer have the potential to improve patient care and outcome. The investigative pace has recently been dramatically enhanced by the availability of the complete human genome sequence and the development of high-throughput technology for comprehensive genetic analysis. The application of genomic scale analysis to the study of prostate cancer has resulted in significant successes, including methods of more precise diagnosis and identification of potential prognostic markers and therapeutic targets. It is clear that these novel technologies and approaches provide many opportunities for biologists and clinicians; however, there are many challenges in moving these discoveries forward.