Pouchitis occurs in up to one half of patients after restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA). Cytomegalovirus (CMV) and Clostridium difficile are among the commonest secondary identifiable etiologies. A 17-year-old male with ulcerative colitis underwent IPAA due to refractory disease. Nine months later he experienced bloody diarrhea and fever. Laboratory testing and endoscopy confirmed pouch inflammation. Testing for C. difficile toxins A and B was positive. Histology revealed affluent inclusion bodies and immunohistochemistry detected reactivity against CMV protein. Treatment with metronidazole and vancomycin offered partial improvement, whereas the addition of gancyclovir led to a successful recovery. One month after completion of treatment symptoms recurred. Repeat testing precluded an identifiable infectious cause and the diagnosis of idiopathic chronic pouchitis was established. The patient is currently on maintenance treatment with the probiotic compound VSL#3.