Graft-versus-host disease (GVHD) affects up to 70% of patients who undergo stem cell transplantation. GVHD is associated with significant morbidity and mortality, and commonly affects the skin, liver, and gastrointestinal (GI) system. Gastrointestinal (GI) manifestations of GVHD include anorexia, nausea, vomiting, abdominal pain, and diarrhea. In patients with GI GVHD, the extent of gut involvement and its relationship to underlying symptoms is unclear. Furthermore, diagnosis requires histologic evaluation that entails cumbersome invasive endoscopic procedures for tissue procurement. Histologic findings that support this diagnosis are nonspecific and have poor sensitivity and specificity. Treatment of GI GVHD is also nonspecific, and has many systemic side effects that account for a large portion of associated morbidity and mortality.