Background: Cytomegalovirus (CMV) infection is a common viral infection in humans with a diverse manifestation, mostly dependent on the host. CMV infection in the immunocompetent host is generally asymptomatic or may present as a mononucleosis syndrome. Infection in immunocompromised patients cause substantial morbidity and mortality.Case representation: We report a rare manifestation of a CMV infection in a 87-year-old male with end-stage renal failure with dialysis dependency and diabetes who presents with diffuse abdominal pain and nausea. Further assessment with a CT scan of the abdomen showed a thickening of the wall of the preterminal ileum, suggestive of focal enteritis. Ileocolonoscopy showed a partial circular ulcerated mucosa of the preterminal ileum, biopsies showed ulcerations, etiology was unknown. A few days later he develops melena and anemia of 7.2 g/dl. Further exploration with gastroscopy was normal. A new colonoscopy showed no abnormalities; however the terminal ileum could not be visualized. An urgent laparotomy was performed because of hemodynamic instability and showed an ulcus of 7 cm with a thickened terminal ileum. An enterectomy of the inflammated part of the ileum was performed. Histopathology of the ulceration showed the presence of CMV inclusions in the vascular endothelium of the capillaires of the ileal segment. Serologic examination showed nonreactive CMV IgM antibodies and IgG antibodies were positive. PCR CMV showed 300 copies/ml (whole blood). Treatment with intravenous ganciclovir was started with good clinical and biochemical response.Conclusions: In the differential diagnosis CMV disease should be considered in any ulceration in the gastro-intestinal tract in the immunocompromised patient.