Expression profiling and proteomics have the potential to transform the management of prostate cancer, identifying new markers for screening, diagnosis, prognosis, monitoring and targets for therapy. Expression profiling has revealed that the majority of prostate cancers contain fusion genes resulting in the upregulation of ETS family transcription factors. New diagnostic markers to replace PSA are being actively sought using a variety of proteomic platforms. Nevertheless, no single molecular marker has yet been discovered that is any more reliable for predicting outcome than histopathological grading. In the future, small custom-built chips will be used to detect a small panel of RNA or protein markers to answer specific questions concerning patient management for each type of cancer.