A 5 1/4 -year-old boy presented with delayed growth, chronic diarrhea, and hypoproteinemia. Clinical presentation, initial laboratory data, and evaluation of an intestinal biopsy specimen suggested a diagnosis of celiac disease. Symptoms did not resolve on a gluten-free diet. The development of hyperammonemia prompted further studies that led to the diagnosis of lysinuric protein intolerance. Lysinuric protein intolerance, although a rare disorder, should be included in the differential diagnosis of conditions associated with intestinal villous atrophy.