Conditioning
Bone marrow eradication treatment
For malignant blood diseases, a high-dose combination of busulfan and cylcophosphamide is given during the last 8 days before the transplant. Busulfan is given for 4 days and cyclophosphamide is given for 2 days. Patients who are not able to take busulfan orally will receive an intravenous preparation. In patients who have had CNS recurrence of acute leukemia, total CNS radiation may be appropriate before the other medications are given.
In special cases, it is recommended to administer fractioned total-body radiation and cyclophosphamide.
Prevention of hemorrhagic cystitis
Byproducts of chemotherapy drugs cause sores and inflammation of bladder mucosa causing bleeding. To prevent this, the following is administered:
- forced hydration – starting before the first dose of busulfan (or cyclophosphamide for total-body radiation) with continual intravenous infusion and measurement of diuresis. Hydration is stopped approximately 20 hours after the last infusion of cyclophosphamide
- mesna – uroprotector given intravenously for prevention of urinary toxicity in connection with administration of cyclophosphamide
Nausea prophylaxis and treatment
Metoclopramide is always given before busulfan and ondansetron is given before cyclophosphamide. Other medications are used in cases where this regimen is insufficient.
Infusion of stem cells
The stem cells are transferred to the recipient via intravenous infusion, as in a normal blood transfusion, or during support (as for HMAS) if the stem cells have been frozen 
.
The stem cells migrate to the recipient's bone marrow where they establish with the help of adhesion molecules and proliferate in a complicated, and far from fully clarified, interaction between cytokines, growth factors, and other cellular interactions.
After 2-4 weeks, the granulocytes will start to appear in the patient's peripheral blood. Effective platelet production usually starts somewhat later.
For ABO incompatibility between the donor and recipient, serious hemolysis may occur. Therefore, antibodies must be removed either by plasmapheresis, if the recipient has antibodies in a high titer against the donor erythrocytes, or by removing the plasma from the donor marrow if the donor has a high titer against the recipient. Sometimes erythrocytes must be removed from the stem cell product.