Most prostate cancers are treated, although more than 80% remain clinically insignificant and fewer than 3% are fatal. This retrospective study of 240 radical prostatectomy cases with comprehensive follow-up was a search for reliable markers of prostate cancer prognosis evaluable on biopsy specimens to enable minimization of unnecessary treatment, morbidity, and costs. Representative cancer and benign tissue from each prostatectomy specimen was made into tissue microarrays and stained with antibodies targeting 20 gene sequences. Traditional clinical and pathologic prognosticators and the 20 antibody stains were correlated with patient outcomes. By univariable analysis 4 of 20 antibodies (STMN1/stathmin 1, CYP4Z1/cytochrome p450-4z1, CDH1/E-cadherin, and Hey2), Gleason score, perineural invasion, and apical involvement were statistically significant outcome predictors for biopsy tissue. By multivariate analysis, Gleason score, Hey2, and CYP4Z1 were independently predictive. STMN1 and CDH1 were not independent of Gleason score but remain useful because marker interpretation is objective and Gleason scores often differ for biopsy and prostatectomy specimens.