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The pathogenesis of inflammatory bowel diseases remains unclear. Genetic and environmental factors are involved. Studies of the association between tonsillectomy and inflammatory bowel disease have yielded conflicting results.PubMed and EMBASE were searched to identify studies evaluating the association between tonsillectomy and inflammatory bowel disease [Crohn's disease (CD) and ulcerative colitis (UC)]. Odds ratios with 95% CI were calculated using a random- or fixed-effects model. The χ2 test and I2 test were used to assess homogeneity. Egger's test was used to evaluate publication bias.Thirteen observational case–control studies including 4122 patients (3035 UC/1087 CD) and 5103 controls were analysed. The summary odds ratio estimated for UC following a tonsillectomy was 0.932, 95% CI 0.819–1.062. The odds ratio for CD following a tonsillectomy was 1.194, 95% CI 0.992–1.437. Publication bias was not detected (Egger's test coefficient −3.50 to 1.55; P = 0.39).No obvious association between tonsillectomy and inflammatory bowel disease was identified in our meta-analysis.