Cases of autism have frequently been reported in association with gastrointestinal problems. These observations have stimulated investigations into possible abnormalities of intestinal microbiota in autistic patients. The objectives of this paper were to review the possible involvement and mechanisms of gastrointestinal microbiota in autistic spectrum disorder and explain the possible role of gastrointestinal microbiota in the condition. This review addresses the possible involvement of bacteria, viruses and fungi, and their products in autism. Direct viral damage of neurons or disruption of normal neurodevelopment by immune elements such as cytokines, nitric oxide and bacterial products, including lipopolysaccharides, toxins and metabolites, have been suggested to contribute to autistic pathology. Numerous intestinal microbial abnormalities have been reported in individuals with autism. Research to date exploring possible gastrointestinal problems and infection in autism has been limited by small and heterogeneous samples, study design flaws and conflicting results. Furthermore, interventions designed to modify the intestinal microbial population of autistic patients are few and limited in their generalisation. In order to bring clarity to this field, high-quality and targeted investigations are needed to explore the role of gastrointestinal microbiology in autism. To this end, several promising avenues for future research are suggested. (C) 2010 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins