For evaluating the therapeutic approaches in the follow-up and complications of patients treated with bone marrow transplantation (BMT), the histopathology is important on many occasions. The authors describe the different morphological changes that have an important role for treatment of these patients, classified according to their target organs of localization: skin, digestive tract, liver, and bone marrow. Graft-versus-host disease (GVHD) mainly affects the skin, gastrointestinal tract, and liver, and is sometimes difficult to differentiate from radiochemotherapy or infectious diseases. In the liver, the most frequent complications are GVHD, veno-occlusive disease, and infections. In the bone marrow, it is most important to evaluate the elimination of hemopathy and the reconstitution of normal hematopoiesis.