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This report presents a case of massive mucosal necrosis of the small intestine in a patient with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), which particularly affects the brain, nervous system and muscles. A 45-year-old Japanese female, with an established diagnosis of MELAS, presented with vomiting. Computed tomography showed portomesenteric venous gas and pneumatosis intestinalis. She underwent a resection of the small intestine. A microscopic study showed necrosis of the mucosa and vacuolar degeneration of smooth muscle cells in the arterial wall. Immunohistochemistry showed anti-mitochondrial antibody to be highly expressed in the crypts adjacent the necrotic mucosa. The microscopic and immunohistochemical findings suggested the presence of a large number of abnormal mitochondria in MELAS to be closely linked to mucosal necrosis of the small intestine.