Allogeneic transplant of hematopoietic stem cells (HSCT) is the only treatment shown to have the capacity to cure MCL. Because of the response seen when patients are given imatinib, HSCT is reserved for younger patients who do not respond to other treatments.

This is the most common transplant type used in leukemia, though it is also the most toxic. With this type of transplant, the patient receives cells obtained from the bone marrow of a donor whose tissue type (known as HLA) is a 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.

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 donor-recipient incompatibility; when this happens, the new immune system deriving from the donor attacks parts of the host's body. The symptoms of GVHD are:

• Severe, itchy skin rash.
• Nausea
• Severe diarrhea
• 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.