BackgroundThere are no published studies on the simultaneous effect of extent and location of positive surgical margins (PSMs) on biochemical recurrence (BCR) after robot-assisted laparoscopic prostatectomy (RALP). The aim was to report the incidence, extent, and location of PSMs over the inclusion period as well as the rates of BCR and cancer-related mortality, and determine if BCR is associated with PSM extent and/or location.MethodsRetrospective review of 530 consecutive patients who underwent RALP between 2003 and 2012. Kaplan-Meier (KM) survival analyses and Cox regressions were performed to determine variables associated with BCR.ResultsFor the 530 operated patients, evaluated at a median of 92 months (IQR, 87–99), PSMs were observed in 156 (29%), of which 24% were focal. Out of 172 PSMs, 126 (73%) were focal and 46 (27%) were extensive. The KM survival using BCR as endpoint was 0.81 (CI, 0.78–0.85) at 5 years and was 0.67 (CI, 0.61–0.72) at 10 years; and using cancer-related mortality as endpoint was 0.99 (CI, 0.99–1.00) at 5 years and 0.95 (CI, 0.92–0.98) at 10 years. Multi-variable analysis revealed the strongest predictors of BCR to be Gleason score ≥ 8 (HR = 7.97; CI, 4.38–14.51) and 4 + 3 (HR = 3.88; CI, 2.12–7.07), lymph nodes invasion (HR = 3.42; CI, 1.70–6.91), pT stage 3b or 4 (HR = 3.07; CI, 1.93–4.90), and extensive apical PSMs (HR = 2.62; CI, 1.40–4.90) but not focal apical PSMs (HR = 0.86; CI, 0.49–1.50; p = 0.586).ConclusionExtensive apical PSMs significantly increased the risk of BCR, independently from pT stage, Gleason score and lymph nodes invasion, while focal apical PSMs had no significant effect on BCR.Electronic supplementary materialThe online version of this article (10.1186/s12885-018-5229-1) contains supplementary material, which is available to authorized users.