A 59-year-old man was referred to our hospital for examination of intermittent abdominal pain. Computed tomography scan showed a cystic lesion adjoining the ileum, and small bowel series demonstrated a small bowel diverticulum. Double-balloon enteroscopy (DBE) revealed a diverticulum in the ileum and a soft and smooth elevated lesion with a small hole at the base of the diverticulum. Small bowel series under DBE demonstrated that the cystic lesion communicated with the diverticulum through the small hole. The diagnosis was Meckel's diverticulum and an omphalomesenteric cyst. This is the first reported case of a Meckel's diverticulum and omphalomesenteric cyst communicating through a small hole without a fibrous ligament. In addition, precise evaluation was possible by small bowel series and DBE.