A 16-year-old man who had been diagnosed with the Peutz-Jeghers syndrome at the age of 8 years presented with crampy abdominal pain. Thorough examinations revealed a large jejunal polyp causing intussusception, as well as multiple polyps in the small and large intestines. Preoperative proctoscopy demonstrated the coexistence of a submucosal tumor in the rectum. Proctoscopic mucosal resection was performed and histological and immunohistochemical examinations led to a diagnosis of carcinoid tumor. Additional transanal resection of the rectal wall showed no residual tumor and the patient has been well for 2 years to date. Although malignant tumors are increasingly reported in association with the Peutz-Jeghers syndrome, to our knowledge, there have been no previous reports of such an association in the English-language and Japanese literature.