The development of drugs to prevent prostate cancer is underway, yet monitoring the potential efficacy of these agents during clinical trials relies on measuring intermediate endpoints. In this review, various candidate markers are presented that are under different stages of evaluation as intermediate endpoint biomarkers. In addition, the near future will bring an unprecedented wave of new potential biomarkers. For instance, through genomics-based methods many new genes are being discovered whose altered expression may be involved in different phases of prostate cancer development and progression. In the development of rational approaches for selecting which of these untested biomarkers may be useful to measure systematically, there must be an improved understanding of the mechanisms of prostatic carcinogenesis. We submit that this improved understanding will come through new knowledge of the biology of normal prostate epithelial cells, the determination of the precise target cells of transformation, and how their growth regulation is genetically and epigenetically perturbed during the phases of initiation and progression. In this review, therefore, we also present our recent immune-mediated oxidant injury and regeneration hypothesis of why and how the prostate is targeted for carcinogenesis.