Introduction There are conflicting data regarding the incidence, site and prognostic significance of positive margins resulting from iatrogenic incision into the prostate (pT2+) or non-iatrogenic inability to excise extraprostatic extension (EPE) of tumor. Materials and methods The surgical specimens were whole-mount processed. Nerve-sparing, tumor extension and Gleason score were considered possible factors involved in positive margins. Time to PSA progression was studied using a Kaplan-Meier product-limit analysis. Results Positive margins resulted from iatrogenic incision in 61/230 (26.52%) prostates and from EPE in 34/230 (14.78%) prostates. The site most frequently involved in pT2+ prostates was the posterolateral quadrants (40.98%); in cases with EPE both anterolateral and posterolateral quadrants (67.65%) were most frequently involved. Positive margins occurred equally in patients with and without nerve-sparing in both groups. Tumors were significantly more extensive and with higher Gleason score in patients with EPE. Time to PSA progression was similar in patients with pT2+ versus EPE and no invasion of the seminal vesicle, but was significantly shorter in patients with EPE and invasion of the seminal vesicle. Conclusion The frequency of positive margins in our institution was similar to others with large experience in performing radical prostatectomies. The higher frequency of posterolateral quadrants in iatrogenic positive margins is probably related to the preservation of adjacent vital structures and not to nerve-sparing surgery. A trend for a decreasing frequency of non-iatrogenic surgical margins may be explained by the marked increase of clinical stage T1c in recent years. More-extensive tumors and higher Gleason scores seem to influence only non-iatrogenic positive margins. Biochemical (PSA) progression in EPE must be studied by stratifying the patients into two groups: with and without seminal vesicle invasion.401105111