Bone marrow transplantation (BMT) has emerged as a major therapeutic option for a number of nonmalignant disorders affecting the bone marrow and leading to clinical manifestations most likely affecting distant organs. Disorders such as autoimmune diseases, metabolic disorders, hemoglobinopathies, immunodeficiencies, and others have been the target of high-dose therapy and autologous or allogeneic bone marrow, stem cell, or cord blood transplantation. Successful results have been reported in a large number of these disorders. In most instances the goal of transplantation is to provide sufficient degree of marrow engraftment to allow long-term amelioration of disease phenotype. For many of these disorders, early diagnosis is crucial in achieving the desired results as transplantation becomes difficult when significant end-organ damage sets in. Major unsolved problems, including toxicity of conditioning regimens, graft-versus-host disease, and donor availability, need to be addressed. We attempt to provide a comprehensive review of BMT and discuss unique features of this modality for treatment of nonmalignant disorders.