Objective. To investigate the incidence, prevalence and the long-term outcome of autoimmune enteropathy in Sweden. Material and methods. In 2002 a questionnaire was sent to all paediatric departments in Sweden asking them to report all known cases of this condition from the period 1985-2002. Results. The response rate was 92%. Five patients were reported and 3 were included in the study. Only one patient fulfilled all the diagnostic criteria and two were considered as possible cases of autoimmune enteropathy. The incidence was 0.06 to 0.12x10-5 and the prevalence was 0.05 to 0.10x10-5 for children aged 0-16 years. At the end of the study period all 3 patients were still alive. Two boys were receiving immunosuppressive treatment and one girl was in remission and functioning well on a gluten-free diet only. One of the patients had adrenalitis. This combination has not been reported previously in autoimmune enteropathy. Conclusions. Autoimmune enteropathy in its severe forms is a rare disease in Sweden. None of the patients reported died during the study period. Comparative studies are difficult as different diagnostic criteria are used to diagnose this disease.