Background: Preoperative staging for prostate cancer underestimates the final pathology stage in approximately 40-50% of the cases. Previous work from our institution demonstrated that an enhanced reverse transcriptase polymerase chain reaction (RT-PCR) assay for prostate-specific antigen (PSA) enabled more accurate staging of presumably localized prostate cancer. The goal of the current study is to determine if needle biopsy results when combined with the RT-PCR for PSA assay are a better predictor of final pathology stage. Methods and Results: One hundred sixty-two men with needle biopsy-diagnosed prostate cancer had blood drawn for the RT-PCR for PSA assay before undergoing radical prostatectomy. Polymerase chain reaction primers specific for the PSA gene were run, along with appropriate controls. Tumor was characterized using the TMN staging system: organ confined (pT2a-c), capsular penetration (pT3a-b), seminal vesicle involvement (pT3c). Surgical margins and lymph nodes were also evaluated. Of the 162 patients, the majority had localized disease by digital rectal examination: T2 = 97% and T3 = 3%. On needle biopsy, 48 cases (30%) had a Gleason score greater than or equal to 7 and 35 cases (22%) had perineural involvement (PNI). The RT-PCR for PSA assay was positive in 50 patients (31%). Final pathology revealed 39% of patients had pT3 disease; none of the 162 patients had lymph node involvement. Statistical analysis revealed that a Gleason score greater than or equal to 7 had 81% specificity and 46% sensitivity in predicting pT3 disease (odds ratio 3.6). The presence of PNI on needle biopsy was 89% specific and 38% sensitive in predicting pT3 disease (odds ratio, 4.9). The RT-PCR for PSA assay was 89% specific and 62% sensitive in predicting pT3 disease (odds ratio, 13.0). All 14 cases with both RT-PCR for PSA and PNI positivity had pT3 disease. Logistic regression analysis demonstrated the independent predictive strength of PNI on needle biopsy, Gleason score greater than or equal to 7, and RT-PCR for PSA positivity for identifying pT3 disease; their combined odds ratio was more than 180. Conclusions: Using the RT-PCR for PSA assay in conjunction with needle biopsy results increases the predictive strength for pT3 disease in patients with presumed organ-confined prostate carcinoma.