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A 5-year-old male with right atrial myxoma without interatrial communication who presented with abdominal pain, vomiting, fever, and guaiac positive stool is reported. He was later found to have ischemia of a jejunal segment necessitating segmental resection. Although his symptoms persisted postoperatively, surgical removal, of a right atrial myxoma was followed by complete resolution of his intestinal symptoms. We demonstrated that the mesenteric vasculitis was of nonembolic origin, and we speculate autoimmune arteritis as a possible mechanism.