Homocystinuria is frequently associated with severe multisystem involvement such as dislocated lenses, skeletal deformities, mental retardation and premature vascular occlusions. Surprisingly, gastro-intestinal involvement has not been described in this disorder. We present a 17 year old boy with homocystinuria due to cystathionine beta-synthase deficiency, who developed severe gastrointestinal involvement, manifested by chronic diarrhoea and acute pancreatitis. The diarrhoea was successfully treated with betaine. Possible pathophysiological mechanisms and suggested treatment are described.