The dose levels used to fight against ALL cause damage to tissue and bone marrow. Hematopoietic progenitor-cell transplantation, also called bone-marrow transplantation, makes it possible to use high doses of chemotherapy or radiotherapy to eliminate the disease. Transplants can be either autologous or allogeneic.

For patients with ALL, the decision of whether to perform a transplant depend on the patient's age, physical condition, and risk of disease reappearance; this risk of relapse depends on the ALL subtype the patient has (phenotype and cytogenetics), leukocyte count, and presence of residual disease following initial treatment. Put another way, the likelihood of a cure with just chemotherapy will affect the decision of whether to perform a transplant. Patients who are very unlikely to be cured with chemotherapy are recommended a transplant.