Gene expression profiles may lend insight into whether prostate adenocarcinoma (CaP) predominantly occurs in the peripheral zone (PZ) compared to the transition zone (TZ). From human prostates, tissue sets consisting of PZ and TZ were isolated to investigate whether there is a differential level of gene expression between these two regions of this gland. Gene expression profiling using Affymetrix Human Genome U133 plus 2.0 arrays coupled with quantitative real-time reverse transcriptase-PCR was employed. Genes associated with neurogenesis, signal transduction, embryo implantation and cell adhesion were found to be expressed at a higher level in the PZ. Those overexpressed in the TZ were associated with neurogenesis development, signal transduction, cell motility and development. Whether such differential gene expression profiles may identify molecular mechanisms responsible for susceptibility to CaP remains to be ascertained.