Recent phase III trial data clearly demonstrate that adjuvant therapy can reduce recurrence and increase survival after prostatectomy for prostate cancer. There is great interest in being able to accurately predict who is at risk of failure to avoid treating those who may not benefit. The standard markers consisting of prostate specific antigen (PSA), Gleason score, and pathological stage are not very specific, so there is an unmet need for other markers to aid in prognostic stratification. Numerous studies have been conducted with various markers and more recently gene signatures, but it is unclear whether any of them are really useful. We conducted a comprehensive review of the literature to determine the current status of molecular markers in predicting outcome after radical prostatectomy.