Allogeneic bone marrow transplantation is becoming increasingly performed for a variety of disorders but primarily for hematological malignancies. Graft-versus-host disease (GVHD), which often involves the GI tract, is one of the most common complications of this type of transplantation. The diagnosis of GI GVHD can be difficult to establish because of the nonspecific nature of associated symptoms, few diagnostic endoscopic findings, and potential difficulty in making a histological diagnosis. In this review, we summarize current concepts and controversies regarding the diagnostic evaluation for GI GVHD.