Bone marrow transplantation has become an accepted treatment for malignancy (particularly leukemia and lymphoma), aplastic anemia, and certain inborn errors of metabolism. Patients require intensive care because of chemoradiation therapy toxicity, a prolonged period of immunosuppression and thrombocytopenia, graft-versus-host disease (GVHD), and the need for parenteral nutrition. Gastrointestinal and hepatic diseases are frequent post-transplant problems. They present with intractable nausea and vomiting, intestinal bleeding, diarrhea, esophageal complaints, abdominal pain, and hepatobiliary symptoms. Our clinical approach to complex transplant patients depends on the timing of signs and symptoms after marrow grafting and on the likelihood that specific disease processes are present. Each of these major problems is covered in this review.