Inflammatory bowel diseases (IBDs) are idiopathic autoimmune diseases that are characterized by inflammation of both the small and large intestine. Although IBD is common in the general population, the pathophysiology remains ambiguous. Clear understanding of IBD pathophysiology would be a major step toward curative treatment in the future. Hyperhomocysteinemia has been associated with multiple autoimmune diseases including IBD, but homocystinuria has not been associated with IBD before. We report a 9-year-old girl with Crohn's disease and homocystinuria. Her gastrointestinal symptoms improved significantly upon classical homocystinuria treatment, and her last colonoscopy showed a pronounced remission. This case supports the inflammatory role of homocysteine in the gastrointestinal tract and the association between hyperhomocysteinemia and IBD manifestations.