Background: Long-term functional results of ileal pouch-anal anastomosis (IPAA) with mucosal proctectomy (MP) for ulcerative colitis (UC) are satisfactory but may be compromised by perianal fistulae. Methods: We analyzed the effect of the level of MP (above or below the dentate line) on the risk of perianal fistulae in 151 patients undergoing IPAA for UC. Results: A postoperative perianal fistula occurred in 12 patients (10 with MP from the level above the dentate line and 2 below). Patients developing perianal fistulae after IPAA were significantly younger at IPAA (23 vs. 32 years, p = 0.015). Age <25 years at UC onset (hazard ratio, HR, 3.5, p = 0.041), age <30 years at IPAA (HR 4.3, p = 0.015) and MP above the dentate line (HR 4.7, p = 0.010) were significant risk factors for perianal fistulae after IPAA. Multivariate analysis showed that age <30 years at IPAA (HR 4.4, p = 0.018) and MP above the dentate line (HR 6.0, p = 0.012) were significant risk factors. Conclusion: IPAA with MP below the dentate line for UC might reduce the risk of postoperative perianal fistulae.