Autoimmune enteropathy is a rare syndrome which, in children in its most severe form, causes severe life-threatening diarrhoea and dehydration. The enteropathy seems to be part of a systemic disorder that can include neonatal diabetes mellitus, haematological abnormalities, severe allergies and eczema. The syndrome characterised by 'immuno-dysregulation, polyendocrinopathy, autoimmune enteropathy, X-linkage' (IPEX syndrome) is the most severe and also the best characterised form of autoimmune enteropathy. Recently, more has been discovered about the pathophysiology of autoimmune enteropathy. It would seem that an immunological defect exists, which is caused by the non-functioning of regulatory T cells. Characteristic of this disorder are circulating auto-antibodies that cause destruction of the intestinal wall. In a number of patients, this defect is caused by mutations in the Foxp3 gene on the X chromosome. The discovery of the molecular background for autoimmune enteropathy provides important new potential opportunities for diagnosis and therapy. Treatment options for this condition are immunosuppression and bone marrow transplantation.