Gastrointestinal and hepatic complications are common in bone marrow transplant recipients. These patients often present difficult diagnostic and therapeutic dilemmas. Toxicity related to chemoradiation and other drugs, graft-versus-host disease, and infections account for the major mechanisms of gastrointestinal and liver damage. The timing of symptom presentation after transplantation is especially important to differentiate between various possible etiologies. There continues to be a paucity of prospective data on the etiology and outcome of specific gastrointestinal symptoms. Despite major advances in this field, significant hurdles still remain. The ability to predict, prevent, and treat gastrointestinal and hepatic complications is crucial for long-term survival. However, new problems, such as secondary malignancies, continue to emerge as survival increases.