A 50-year-old Japanese female was admitted to our hospital because of ileus due to Chilaiditi syndrome. Her symptoms did not improve with conservative therapy, so chest and abdominal computed tomography (CT) was performed on the fifth day after hospital admission. A diagnosis of incarceration of a right diaphragmatic hernia was established in the coronal view of CT, and emergency surgery was performed. A dilated loop of small intestine was seen in the right thoracic cavity, which was strangulated by the 2-cm defect in the diaphragm. Primary closure of the diaphragm was performed. Approximately 80 cm of the terminal ileum showed obvious ischemic changes, and it was cut and reconstructed. Postoperatively, the patient made an uneventful recovery and was discharged on the 15th postoperative day. A histological examination of the specimen of the diaphragm around the hernia orifice showed the presence of a small cystiform glandular system with hemorrhage and congestion. These findings indicated that heterotopic endometriosis was present in the diaphragm. This report describes the first known case of right diaphragmatic hernia secondary to heterotopic endometriosis in a patient with Chilaiditi syndrome. The clinical course and management of affected patients and a literature review of these three unusual conditions are discussed.