We describe a 42-month-old child with protracted diarrhoea that began at 6 months of age. Severe secretory diarrhoea persisted despite therapy with exclusion diets, total parenteral nutrition, chemotherapeutics, antisecretory drugs. The diagnosis of autoimmune enteropathy with total villous atrophy and anti-enterocyte antibodies was established at 16 months of age. Prednisone therapy induced a clinical remission. After dose reduction, clinical relapse occurred, complicated with HCV infection with elevated serum alanine aminotransferase activity. Increasing the prednisone dose did not result in clinical improvement. Treatment with cyclosporine induced clinical remission. After 10 months cyclosporine therapy is still continued and the boy is doing well.