In this review, a series of relatively well-documented ancillary biomarkers and emerging molecular assays are evaluated for their relative ability to predict prognosis in prostate cancer. Prognostic factors that have achieved widespread use and classified as Category I by the College of American Pathologists Solid Tumor Prognostic Factor Consensus Conference are compared with newer tests that are beginning to be used in clinical practice (Category II) and emerging molecular-based assays that have yet to be widely validated in the published literature or clinical trials (Category III).