Relative gene expression of the estrogen receptors (ER)-alpha (NR3A1) and ER-beta (NR3A2) along with progesterone receptors PR-A and PR-B (NR3C3) was determined by quantitative real-time PCR in a previously characterized panel of paired human prostate tumor and surrounding unaffected tissue (Prostate 54:275). In approximately half of these cases, a 10-fold or greater reduction in the relative mRNA levels of ER-beta but not ER-alpha was found in the cancer as compared to normal tissue, which was also observed with unpaired samples. Immunohistochemical staining for ER-beta and ER-alpha closely paralleled mRNA expression patterns for both receptors in paired samples. Reduced relative expressions of PR-B and total PR-A and PR-B isoforms were also observed in prostate tumor as compared to unaffected tissue, implying a potential role of PR in prostate tissue. The relative decrease in ER-beta is greater than that observed in prior studies, suggesting that paired samples more accurately reflect differences within individual cases. These findings favor the concept that ER-beta mediates anti-proliferative signals and its loss in prostatic tumor promotes proliferation of these cells.