Introduction: Gastrointestinal (GI) cytomegalovirus (CMV) infection coexisting with or followed by a diagnosis of inflammatory bowel disease (IBD) is infrequently reported. Not recognizing this condition may delay IBD diagnosis in patients with GI-CMV disease who do not or partially respond to antiviral agents, which could consequently result in unsatisfied treatment outcomes. Patient concerns: Two immunocompetent patients with no known underlying GI conditions presented with acute bloody diarrhea. The first patient developed diarrhea and hematochezia after admission to intensive care unit (ICU) because of severe alcoholic pancreatitis for 10 days duration. Computed tomography abdomen showed segmental jejunal thickening. The other patient presented with a 1-week history of severe bloody diarrhea which required ICU admission. Colonoscopy showed multiple ulcers along terminal ileum and colon. Diagnosis: These 2 patients were initially diagnosed with CMV jejunitis and ileocolitis, respectively, based on endoscopic and histopathologic findings. Both had partial response to treatment with 3 weeks of intravenous ganciclovir. Crohn disease was suspected because of persistent ulcerations on the follow-up endoscopy with the presence of pathological features of chronic inflammation and disappearance of previously detected CMV-infected cells. Intervention: Both patients were treated with systemic corticosteroids and azathioprine. Outcomes: Both patients had complete clinical improvement. Prednisolone could be tapered off in 6 months. Follow-up video capsule endoscopy (VCE) at 6 months showed improvement of mucosal inflammation and ulcers, but neither were completely healed in the first patient. Follow-up colonoscopy at 6 months showed complete resolution of ulcers and inflammation in the second patient. Lessons: IBD should be suspected in patients with a diagnosis of GI-CMV disease who are immunocompetent and have a partial response to antiviral agents. This clinical scenario could be caused by either CMV infection activating immune response resulting in IBD onset, or CMV infection superimposed on pre-existing latent IBD.