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To review interactions between the microbiota and the host in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), emphasizing areas of commonality and divergence.Several lines of evidence support a role for the microbiota in the pathogenesis of IBS and IBD. Some implicate the microbiota in a general sense and relate to variations in the composition of the microbiota between IBS, IBD and controls; others relate to the ability of events and interventions that disrupt/modify the microbiota to predispose to the development of IBS and IBD and, others still refer to reports of the ability of antibiotics, prebiotics or probiotics, in selected circumstances, to beneficially alter their clinical course. Enthusiasm for a role for a specific organism in precipitating disease has been largely (and contentiously) linked to IBD. Many issues remain unresolved and must wait for the application of modern microbiological techniques to well characterized populations and well matched controls.It makes sense, given the size and complexity of the microbiota and its role in homeostasis, that the microbiota and its interactions with the host would play a role in the pathogenesis of IBS and IBD; sorting out the details has proven challenging but does offer new therapeutic avenues for both disorders.