This is the most common transplant type used in leukemia, though it is also the most toxic and involves the greatest risk for the patient. With this type of transplant, the patient receives cells obtained from the bone marrow of a donor who has a set of proteins (known as HLA) that is an exact or near-exact match to that of the patient. The more compatible the tissues, the more likely the transplanted cells are to produce new blood cells.

This type of transplant plays an important role in the first complete remission and is the only available therapy option for patient with recurrent disease.

Close family members such as siblings are the best candidates for allogeneic transplants, though if there is no family member available, the stem cells can be obtained from an unrelated donor. However, complications are more common when the stem cells come from an unrelated donor; the most common such complication is graft-versus-host disease (GVHD).

GVHD is caused by differences between the donor and recipient; when this happens, many of the patient's organs are attacked by the immune system derived from the donor. The symptoms of GVHD are:

• Skin eruptions of differing extension and severity, either with or without itchiness.
• Nausea and vomiting
• Diarrhea of differing degrees of severity.
• Yellowing of the skin and the conjunctiva of the eye (jaundice)
• Fatigue
• Muscle pain

However, GVHD is usually accompanied by a potent reaction against leukemia cells leading to complete elimination of these cells; this phenomenon is called graft-versus-leukemia effect.

For this reason, slight GVHD can be considered beneficial in some cases.