Using bioinformatic and genomic approaches, we have identified several candidate genes that are differentially expressed in prostate cancer. The LifeSeq (Incyte Pharmaceuticals) DNA expressed sequence tag database consists of more than 6.4 million tags obtained from 1,317 complementary DNA libraries made from various tissues (normal and diseased). Using a bioinformatic approach, we looked for candidate genes that show a strong specificity for expression in prostate tissue and also a significant upregulation in cancerous tissue compared with normal tissue. In parallel we constructed several subtraction cDNA libraries using suppressive hybridization protocols (Clontech). These libraries are being sequenced and analyzed. To date a total of 81 genes have been chosen as candidates for further expression analysis. Expression analysis of these candidate genes involved the use of a sensitive Taqman quantitative polymerase chain reaction assay that further determined the tissue-specific expression and whether higher levels of expression are indicative of prostate cancer. Expression analysis data using RNA from different tissues and disease states (approximately 200 samples) helped rank these candidates. A total of eight candidate genes (Arg2, Pro101, Pro108, Pro111, Pro118, Pro119, Pro121, Pro130) were selected for further analysis. A majority of these have been cloned and expressed in bacteria. Monoclonal antibodies are available for two of them, and immunoassays will be developed shortly. These candidates, either individually or grouped in panels, have the potential to become new prostate cancer biomarkers for early detection, differential diagnosis, disease monitoring and disease surveillance.