Short-chain fatty acids (SCFA) affect local and remote motility of the gastrointestinal tract by mechanisms that are not completely understood. In the large intestine where they are produced, they inhibit peristaltic activity and may stimulate tonic activity. When present in the terminal ileum as a result of reflux of colon contents, they elicit propulsive contractions. These local motor effects could involve a neuro-hormonal sensory mechanism located in the mucosa of the terminal ileum and proximal colon. Finally, through a humoral pathway probably involving polypeptide YY release, ileal and colonic SCFA modify upper motility by inducing relaxation of the proximal stomach and lower oesophageal sphincter and reducing gastric emptying. One characteristic feature of the SCFA effects is the dose-dependency of the gastrointestinal motor responses. Indeed, the effects occur only below or above a threshold of SCFA concentration in lumen contents. One putative physiological role of the motor effects of SCFA might be to maintain the physico-chemical balance of the lumen environment in the terminal ileum and proximal colon. Another role might be to co-regulate motility of the upper intestine. The clinical relevance of these effects is unclear. However, some recent findings suggest that excessive SCFA concentrations might induce adverse effects on gastrointestinal and colonic motility and sensitivity in certain diseases such as inflammatory bowel disease and gastro-oesophageal reflux disease.