Gastrointestinal (GI) manifestations of post-natally acquired cytomegalovirus (CMV) in preterm neonates can vary from mild diarrhoea to severe necrotising enterocolitis. However, the suspicion of CMV-related GI disease remains low. Mild CMV disease localised to the GI tract may go undiagnosed initially until a more obvious complication such as strictures manifest. A case of CMV-associated enteritis in an extremely preterm neonate is presented. The diagnosis was established after the histopathology of the surgical specimen showed the presence of CMV inclusion bodies. Testing the stool specimen for CMV to establish the diagnosis when the pathology is limited to the GI tract is also discussed.