We report an 11-year-old boy with fetal alcohol syndrome and immunodeficiency, whose longstanding malnutrition, diarrhoea with steatorrhoea, symptomatic electrolyte loss and eosinophilia were attributed to renal tubular disease and recurrent worm infestation. The symptoms resolved with diagnosis and treatment of infection by the protozoan Isospora belli, although immunodeficiency persisted.