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Treatments that target alterations in gut microbiota may be beneficial for patients with irritable bowel syndrome (IBS). A systematic review and meta-analysis was conducted of randomised clinical trials (RCTs) evaluating the efficacy and safety of probiotics, prebiotics and synbiotics. Factors considered in the analysis included global IBS symptoms and/or abdominal pain, secondary symptoms and the frequency of adverse events. A total of 33 RCTs involving 4,321 patients were identified. Overall, probiotics significantly improved global IBS symptoms compared to placebos (standardised mean difference = −0.32, 95% confidence interval: −0.48 to −0.15; P <0.001), with significant heterogeneity between studies (I2 = 72%; P <0.001). This remained apparent in both single- and multi-strain probiotic interventions as well as synbiotic formulations. However, evidence regarding prebiotics was scarce. There were no significant inter-group differences in terms of the frequency of adverse events. Future RCTs should address methodological limitations, including short follow-up periods and patient adherence.