The present case involves unique enteritis forming multiple ulcers associated with Epstein-Barr virus (EBV). A 57-year-old man had undergone a reduced intensity allogeneic stem cell transplantation for a relapse of multiple myeloma following sequential autologous peripheral blood stem cell transplantation. The ileum, resected for massive melena, showed multiple irregular ulcers with occasional cobblestone-like appearance. There was inflammation including numerous plasma cells in the ulcer bases and surrounding areas, where many EBV-infected plasma cells were detected by double staining with EBV-encoded small RNA-1 (EBER-1) in situ hybridization and CD79a, while EBV-infected epithelial cells were not noted. The number of EBER-1-positive cells in the ileum (mucosa, 1451 cells/mm(2); submucosa, 465 cells/mm(2)) was much larger than in control samples (malignant lymphoma or leukemia after allogeneic stem cell transplantation, n = 4, range 0-113 cells/mm(2); malignant lymphoma after chemotherapy, n = 14, range 0-0.89 cells/mm(2); colon cancer, n = 12, range 0-3.5 cells/mm(2)). In the mucosa near the ulcers, EBER-1-positive cells often surrounded and involved the glandular epithelium, forming lymphoepithelial-like lesions. The histological findings differ from post-transplant lymphoproliferative disorders or intestinal thrombotic microangiopathy, and this is the first case of EBV-associated enteritis with ulcers characterized by numerous plasma cells and lymphoepithelial-like lesions after stem cell transplantation.