The gastrointestinal tract is one of the common targets of acute graft-versus-host disease (GVHD), but accurate diagnosis is difficult because of the nonspecific nature of complicated diseases and the lack of diagnostic findings by conventional endoscopy. Recently, a magnifying endoscope has been developed and used for examining microstructures of the mucosa. Herein, we report the first use of a magnifying endoscope for a patient with gastrointestinal (GI) GVHD. Magnified endoscopic findings of atrophic and coalescent villi of the terminal ileum reflect histological findings of GVHD. Magnifying endoscopy of the terminal ileum may be useful for early detection and follow-up of GI GVHD.