Background Whether inflammatory bowel disease patients are at increased risk of colonoscopic perforations remains controversial. Aim of this study was to investigate whether these patients are at increased risk of perforations. Methods Electronic charts of all patients enrolled in the Nancy IBD cohort (1999–2012) were reviewed. All non-inflammatory bowel disease patients who underwent colonoscopy (1999–2012) were used as controls. Results Of 17,992 colonoscopies, 2375 (13.2%) were performed for inflammatory bowel disease: 1547 for Crohn's disease and 828 for ulcerative colitis. Four IBD patients (0.168%) experienced perforation. Perforation occurred in the sigmoid colon (n = 3) and right colon (n = 1) during disease monitoring or colonic stenosis dilatation. Three patients underwent surgery (2 stomas and no death). Colonoscopic perforation occurred in 16/15,617 controls (0.102%): colonic cancer diagnosis (n = 5, 31.3%) or dilatation (n = 2, 12.5%), polypectomy (n = 5, 31.3%) or mucosectomy (n = 1, 6.3%), and follow-up after diverticulitis (n = 2, 12.5%). Perforation rate was not different between IBD and controls (p = 0.57). Perforations occurred in the sigmoid colon (n = 10, 62.5%), the right colon (n = 4, 25%) and the rectum (n = 2, 12.5%). Twelve controls underwent surgery (9 stomas and one death). Conclusion In this referral centre-based cohort, inflammatory bowel disease patients were not at increased risk of colonoscopic perforation compared to non-IBD controls.