Functional gastrointestinal disorders are common worldwide, are of unknown etiology, and, though non-fatal, may result in considerable impairment in quality of life. For some, a plausible hypothesis which suggests a role for the gut microbiota in their pathogenesis has been advanced. Examples include the role of Helicobacterpylori in functional dyspepsia (FD), the phenomenon of post-infectious irritable bowel syndrome (IBS), and descriptions of qualitative and quantitative alterations in the microbiota in IBS and chronic constipation. While probiotics have been used on an empiric basis by sufferers for the relief of a variety of functional symptoms for decades, it is only recently that large-scale clinical trials have been performed. While positive trends have emerged in a number of areas (alleviation of eradication therapy-related adverse events in FD, overall symptom relief, and reductions in bloating and flatulence in IBS), more large, high-quality, long-duration studies are required in most areas.