ObjectiveTo investigate the bidirectional causal relationship between metabolic syndrome (MS) and inflammatory bowel disease (IBD) using Mendelian randomization (MR). MethodsWe extracted genetic variants with strong correlations from genome-wide association study data on MS as instrumental variables. Inverse variance weighting, MR-Egger regression methods, and weighted median methods were used to estimate the causal effect of MS and risk of developing IBD. ResultsInverse variance weighting found that genetically predicted MS was associated with an increased risk of developing IBD overall (OR=1.113, 95%CI 1.020 to 1.216, P=0.017) and Crohn's disease (OR=1.195, 95%CI 1.072 to 1.333, P=0.001). And inverse MR analysis found an association between ulcerative colitis and an association with a reduced risk of developing MS (OR=0.969, 95%CI 0.948 to 0.991, P=0.005). ConclusionThe results based on MR analysis suggest that genetically predicted MS is associated with the risk of IBD as a whole and Crohn's disease and ulcerative colitis is associated with a reduced risk of developing MS.