Purpose: Cytomegalovirus (CMV) infection is common in immunocompromised patients. Enterocolitis caused by CMV infection can lead to perforation and bleeding of the gastrointestinal (GI) tract, which requires emergency operation. We investigated the demographics and outcomes of patients who underwent emergency operation for CMV infection of the GI tract. Methods: This retrospective study was conducted between January 2010 and December 2020. Patients who underwent emergency GI operation and were diagnosed with CMV infection through a pathologic examination of the surgical specimen were included. The diagnosis was confirmed using immunohistochemical staining and evaluated by experienced pathologists. Results: A total of 27 patients who underwent operation for CMV infection were included, 18 of whom were male with a median age of 63 years. Twenty-two patients were in an immunocompromised state. Colon (37.0%) and small bowel (37.0%) were the most infected organs. CMV antigenemia testing was performed in 19 patients; 13 of whom showed positive results. The time to diagnose CMV infection from operation and time to start ganciclovir treatment were median of 9 days. The reoperation rate was 22.2% and perforation was the most common cause of reoperation. In-hospital mortality rate was 25.9%. Conclusion CMV infection in the GI tract causes severe effects, such as hemorrhage or perforation, in immunocompromised patients. When these outcomes are observed in immunocompromised patients, suspicion of CMV infection and further evaluation for CMV detection in tissue specimens is required for proper treatment.