Growing evidence confirms that up to 95% of autistic children suffer with the dysfunctions of the gastrointestinal (GI) system. We discuss the cellular and molecular mechanisms underlying these disturbances. Some researchers, physicians, and health care professionals suggest that beneficial effects of dietary intervention on behavior and cognition of some autistic children indicate a functional relationship between the GI tract (GIT) and the CNS pathology of ASD. A possible genetic cause for the association of autism and GI disease is discussed. GI disorders are not included in diagnostic criteria for ASD. Clinical and practical experiences provide the support for association between inflammatory bowel disease and ASD.