Emerging data from epidemiologic, microbiome, and physiology research in patients with functional bowel disorders (FBDs) provide evidence for a linkage between alterations in the intestinal microbiota and FBDs. However, currently most of the data is based on association studies, and the causality role of the microbiota in these disorders is not established. Growing evidence for compositional changes and the increasing recognition of the association between the intestinal microbiota and gut-brain functions that are relevant to the pathophysiology and/or clinical symptoms of FBDs have led to increased interest in manipulating the intestinal microbiota for the treatment of these disorders.