Prostate cancer is the most common malignancy in men and is the cause of considerable morbidity and mortality. There is therefore a major incentive to try to identify genes that could be reliable early diagnostic and prognostic markers and therapeutic targets. Recent studies have identified a number of genes that discriminate prostate tumor from nontumor samples. However, prostate tissue contains several cell types such as glandular epithelial cells, stromal cells, and cells of other supporting structures interspersed with neoplastic and hypertrophic epithelial cells. Gene expression differences derived from categorically labeled, tumor and nontumor, prostate samples may primarily reflect varying proportions of the nonneoplastic prostate components.