A 42-year-old man experienced frequent dysphagia, severe nausea, incessant vomiting, and weight loss from the 14th day after human leukocyte antigen-matched sibling allogeneic hematopoietic cell transplantation when donor-derived hematopoiesis was reconstituted. The patient’s digestive medical history was not available. The symptoms could not be alleviated with symptomatic treatment. Esophagogastroscopy revealed multiple ulcerations on the wall of the esophagus without a covering pseudomembrane (A). Endocytoscopy (GIF-H290EC; Olympus, Tokyo, Japan) and double staining with methylene blue and crystal violet was performed for further evaluation. The endocytoscopic images showed that the esophageal epithelial cells were shrunken, with pyknosis and with diffuse lymphocytes infiltration (B). We diagnosed the lesions as acute graft-versus-host disease (GVHD), and 1 mg/kg/day methylprednisolone was initiated immediately. The symptoms were resolved in 1 week. Two weeks later, the pathologic findings were consistent with the endocytoscopic findings (C, H&E, orig. mag. × 400). Follow-up esophagogastroscopy (D, left) and endocytoscopy (D, right) showed healing of the ulcerations.