The Pb-PRL transgenic mice that overexpress the rat prolactin (PRL) gene specifically in the prostate develop a dramatic enlargement of the prostate gland. The objective of this study was to characterize the molecular mechanisms involved in the prostate hyperplasia seen in the Pb-PRL transgenic mice. cDNA microarray analysis was used to identify differentially expressed transcripts in the hyperplastic prostates of 6-months-old transgenic mice compared with age-matched controls. We report the identification of 266 genes (175 up-regulated and 91 down-regulated) that were differentially expressed in the enlarged transgenic prostates compared with controls. Subsequential real-time RT-PCR was used to verify a set of differentially regulated transcripts. The hyperplastic prostates of Pb-PRL transgenic mice demonstrate a molecular pattern supporting the importance of reduced degree of apoptosis for the development of the phenotype. Immunohistochemical analysis of apoptotic activity, using 2 different markers of apoptosis (ssDNA and activated caspase-3), were performed, and the results showed a diminished apoptosis activity in the prostate of Pb-PRL transgenic mice compared with control prostates. The increased stromal/epithelial ratio of the Pb-PRL transgenic prostate, together with up-regulation of a significant fraction of genes involved in tissue remodeling activity, including synthesis and degradation of the ECM and changes in protease activity, suggests that activation of the stroma is involved in the development of the prostate hyperplasia. Overall, the differentially expressed transcripts identified in this study, show many molecular similarities between the prostate hyperplasia of PRL-transgenic mice and human prostate pathology including both BPH and prostate cancer.