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There is direct evidence that the pathogenesis of inflammatory bowel disease (IBD) involves the gastrointestinal microbiota and some evidence that the microbiota might also play a similar role in irritable bowel syndrome (IBS). The aim of this article is to review the emerging evidence for the mechanisms and effectiveness of probiotics in the management of these disorders.The composition of the gastrointestinal microbiota is strongly influenced by factors including age, diet and disease. Probiotics may be effective through their impact on the host gastrointestinal microbiota and promotion of mucosal immunoregulation. Probiotics are considered to be well tolerated, although the quality of studies and health claims has been variable. There are many short-term studies demonstrating the effectiveness of probiotics in IBS, although recommendations should be made for specific strains and for specific symptoms. Within IBD, a number of trials have shown the benefits of a range of probiotics in pouchitis and in ulcerative colitis, although current evidence in Crohn's disease is less promising.Clearly, some probiotics have considerable potential in the management of IBS and IBD; however, the benefits are strain specific. High-quality trials of probiotics in gastrointestinal disorders as well as laboratory investigations of their mechanism of action are required in order to understand who responds and why.