We report a case of haemangioma of the small intestine complicated by protein-losing gastroenteropathy. A 32-year-old female had suffered from hypoproteinaemia for 6 years, but the cause of this condition had not been determined. On diagnosis and therapy for hypoproteinaemia, intra-operative endoscopy and histological examination were performed and she was subsequently diagnosed with capillary haemangioma of the small intestine. Angiography was not useful for the detection of capillary haemangioma of the small intestine in this case. Although intestinal haemangioma is an important cause of gastrointestinal bleeding, protein loss is an extremely rare complication and this case is the first to be reported in Japan.