Success in transplanting blood stem cells depends on finding a compatible match of the antigens on donor's cells and tissues with those on the patient's. In most cases, this means finding sets that are slightly different, but not too different. Donors need not be related to the patient, but they must have a reasonable amount of compatibility. A blood test known as "tissue typing" is used to find good matches.

When patients donate their own stem cells (autologous), "self" antigens meet "self" antigens and there is enough similarity to lessen the risk of immune cell warfare. The same advantages are associated with syngeneic (from identical twin) transplants, although few patients have identical twins.

In most cases, the transplant is allogeneic, meaning the blood-forming stem cells come from a "non-self" donor. These transplants will contain antigens that are somewhat like--but not identical to--those of the patient.