The prognostic implications of capsular incision (CI) remain to be defined. We evaluated the impact of CI on biochemical recurrence (BCR) and the potential risk factors of CI. Between June 1995 and July 2007, 266 patients with follow-up for at least 6 months, who had neither the seminal vesicle nor lymph node involvement on prostatectomy specimen, were included. Patients with insufficient biopsy data and those with neoadjuvant and/or adjuvant therapy were excluded. CI was defined as tumor extending into the inked margins, at sites except the apex of the prostate, without documented extraprostatic extension (EPE). There were 186 with organ-confined disease and negative surgical margins (pT2/SM-), 12 with organ-confined disease and an apex-only positive margin (pT2/AM þ ), 35 with CI, 19 with EPE and negative surgical margins (pT3a/SM-) and 13 with EPE and positive surgical margins (pT3a/SM þ ). We compared BCR-free probability among these five groups and the risk factors for CI were assessed. The 3-year BCR-free probability for each group was 92.7% for pT2/SM-, 75.8% for pT2/AM þ , 70.7% with CI, 84% with pT3/SM-and 51% in pT3/SM þ . That for CI was worse than pT2/SM-(P ¼ 0.007), not significantly different from pT2/AM þ and pT3/SM-(P ¼ 0.614, P ¼ 0.318, respectively), but better than pT3/SM þ (P ¼ 0.044), adjusting for the pre-operative prostate-specific antigen and pathological Gleason score. The risk for CI was significantly associated with more than 25% positive biopsy cores. CI seems to affect BCR and is more likely to occur in proportion to positive biopsy cores.