Background: Anal ulcerations are frequently observed in Crohn's disease (CD). However, their natural history remains poorly known, especially in pediatric-onset CD. Methods: All patients with a diagnosis of CD before the age of 17 years between 1988 and 2011 within the population-based registry EPIMAD were followed retrospectively until 2013. At diagnosis and during follow-up, the clinical and therapeutic features of perianal disease were recorded. An adjusted time-dependent Cox model was used to evaluate the risk of evolution of anal ulcerations towards suppurative lesions. Results: Among the 1,005 included patients (females, 450 (44.8%); median age at diagnosis 14.4 years (IQR, 12.0-16.1)), 257 (25.6%) had an anal ulceration at diagnosis. Cumulative incidence of anal ulceration at 5 and 10 years from diagnosis was 38.4% (CI95%, 35.2-41.4) and 44.0% (CI95%, 40.5-47.2), respectively. In multivariable analysis, the presence of extra-intestinal manifestations (Hazard Ratio (HR) 1.46, CI95% 1.19-1.80, p=0.0003) and upper digestive location (HR 1.51, CI95% 1.23-1.86, p<0.0001) at diagnosis were associated with the occurrence of anal ulceration. Conversely, ileal location (L1) was associated with a lower risk of anal ulceration (L2 vs L1 HR 1.51, CI95% 1.11-2.06, p=0.0087; L3 vs L1 HR 1.42, CI95% 1.08-1.85, p=0.0116). The risk of fistulizing perianal CD was doubled in patients with a history of anal ulceration (HR 2.00, CI95% 1.45-2.74, p<0.0001). Among the 352 patients with at least one episode of anal ulceration without history of fistulizing perianal CD, 82 (23.3%) developed fistulizing perianal CD after a median follow-up of 5.7 years (IQR, 2.8-10.6). In these patients with anal ulceration, the diagnostic period (pre vs biologic era), exposure to immunosuppressants and/or anti-TNF did not influence the risk of secondary anoperineal suppuration. Conclusion: Anal ulceration is frequent in pediatric-onset CD, with nearly half of patients presenting with at least one episode after 10 years of evolution. Fistulizing perianal CD is twice as frequent in patients with present or past anal ulceration.