Cytomegalovirus (CMV) infection of the gastrointestinal tract is common in immunosuppressed patients; however, small bowel perforation from tissue-invasive CMV disease after many years of immunosuppressive therapy is a rare complication requiring timely medical and surgical intervention. We report a case of a postrenal transplant patient who presented to the emergency department with severe lower abdominal pain with CT of the abdomen/pelvis revealing a small bowel perforation. He underwent an emergent laparoscopic right hemicolectomy, and his histopathology of the terminal ileum was positive for CMV disease. He was successfully treated with intravenous ganciclovir postoperatively. We discuss the pathophysiology, histopathological features and treatment of CMV infection.