BACKGROUND: Colonoscopy is commonly performed in patients with irritable bowel syndrome (IBS) to rule out organic disease. We performed a meta-analysis to assess the prevalence of organic disease detected at colonoscopy in IBS and its potential risk factors. METHODS: Medline, Embase, and Web of Science were searched through January 2022. Observational studies that reported diagnostic yield of colonoscopy for organic disease including colorectal cancer (CRC), inflammatory bowel disease (IBD), or microscopic colitis (MC) in adult IBS patients were eligible. Pooled prevalence and risk difference (RD) with 95% confidence intervals (CIs) were calculated. RESULTS: Of 2490 citations identified, 12 studies were eligible containing 28,630 patients with IBS undergoing colonoscopy. Pooled prevalence of CRC, IBD, and MC in IBS was 0.78%, 4.48%, and 2.35%, respectively. No difference in the yield for CRC, IBD, and MC was seen between IBS and non-IBS patients. CRC was rare in IBS patients without alarm symptoms or younger than 40 years (<0.1%). Pooled Prevalence of CRC (2.47% vs. 0.11%; RD 2.57%, 95% CI 0.37%-4.78%) and IBD (8.86% vs. 4.25%; RD 10.75%, 95% CI 4.81%-16.68%) was significantly higher in IBS patients with alarm symptoms compared with those without. IBD and MC were more likely to be detected at colonoscopy in IBS-D compared with IBS-C. The prevalence of CRC and MC was higher in IBS patients with older age than younger age. CONCLUSION: We provide the first pooled estimate of yield of colonoscopy in IBS and its risk factors, which may be used to inform clinical decision and support guidelines.