Gastrointestinal (GI) graft-versus-host disease (GVHD) and cytomegalovirus (CMV) infection often simulate each other. However, distinction between GVHD and CMV infection is critical in the management of immunosuppression for transplant recipients. This study retrospectively reviewed 16 patients diagnosed with GVHD from 2010 to 2016 and found 4 cases (25%) coinfected with CMV. Two cases were initially diagnosed as GVHD only but found to have CMV infection by serological testing within 3 days after immunosuppression treatment for GVHD. The remarkable histological feature of CMV infection appeared to be significant acute inflammation in addition to apoptotic epithelial injuries, and particularly in an early stage of CMV replication, acute inflammation is possibly the only detectable feature of CMV infection.