The ability to distinguish indolent from aggressive prostate tumors remains one of the greatest challenges in the management of this disease. Ongoing efforts to establish a panel of molecular signatures, comprising gene expression profiles, proteins, epigenetic patterns, or a combination of these alterations, are being propelled by rapid advancements in 'omics' technologies. The identification of such biomarkers in biological fluids is an especially attractive goal for clinical applications. Here, we summarize recent progress in the identification of candidate prognostic biomarkers of prostate cancer using biological fluid samples.