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The article presents information on a case of gastrointestinal toxicity when substituting Methotrexate (MTX) with Mycofenolate Mofetil (MMF) for the prevention of graft-versus-host disease in stem cell transplantation following myeloablative conditioning. While studying such case on the patients, the authors observed a decreased incidence of severe mucositis and length of hospitalization, which can be interpreted as a consequence of the substitution of MMF for MTX. It was found that the patient group receiving CSA/MTX had chronic myelogenous leukemia (65%) whereas this group represented only 38% in the CSA/MMF group. According to the authors, it is very likely that the proportions of the peripheral blood stem cells and the bone marrow are not equally balanced which may lead to a longer time to hematopoietic reconstitution in the group including more marrow transplants.