We report the clinical course of a case of X-linked lissencephaly with absent corpus callosum and abnormal genitalia (XLAG) exhibiting severe diarrhea. The patient demonstrated lactose intolerance and his intractable seizures were relieved with lactose-free, extensively hydrolyzed whey protein formula. At the age of 2 years while being treated with the antiallergic formula, he was affected with severe diarrhea that resembled watery diarrhea-hypokalemia-acidosis syndrome (WDHA). Administration of octreotide was effective in relieving his secretory diarrhea. Hypoglycemia without hyperinsulinemia was seen during fasting, and plasma vasoactive intestinal polypeptide was not increased when he had WDHA-like diarrhea. Although pancreas of ARX mutant mice revealed an increased number of beta and delta cells, we did not detect the cause of hypoglycemia and secretory diarrhea by pancreatic endocrinology. His urinary findings mimicked the symptoms of Fanconi syndrome, so it was possible that his hyperaldsteronemia affected not only his intestinal tract, but also his renal tubules.