[4][5] It is most often performed for patients with certain cancers of the blood or bone marrow, such as multiple myeloma, leukemia, some types of lymphoma and immune deficiencies.

As survival following the procedure has increased, its use has expanded beyond cancer to autoimmune diseases[7][8] and hereditary skeletal dysplasias, notably malignant infantile osteopetrosis[9][10] and mucopolysaccharidosis.

[11] Indications for stem-cell transplantation are: Many recipients of HSCTs are multiple myeloma[15] or leukemia patients[16] who would not benefit from prolonged treatment with, or are already resistant to, chemotherapy.

Non-myeloablative, so-called mini transplant (microtransplantation) procedures, have been developed requiring smaller doses of preparative chemotherapy and radiation therapy, allowing HSCT to be conducted in the elderly and other patients who would otherwise be considered too weak to withstand a conventional treatment regimen.

[2] Autologous transplants have the advantage of lower risk of infection during the immune-compromised portion of the treatment, since the recovery of immune function is rapid.

[35] To limit the risks of transplanted stem-cell rejection or of severe graft-versus-host disease in allogeneic HSCT, the donor should preferably have the same HLA-typing as the recipient.

To cryopreserve HSCs, a preservative, dimethyl sulfoxide, must be added, and the cells must be cooled very slowly in a controlled-rate freezer to prevent osmotic cellular injury during ice-crystal formation.

A newer treatment approach, nonmyeloablative allogeneic transplantation, also termed reduced-intensity conditioning (RIC), uses doses of chemotherapy and radiation too low to eradicate all the bone-marrow cells of the recipient.

[46] This leads to a state of mixed chimerism early after transplant where both recipient and donor HSC coexist in the bone marrow space.

[47] Decreasing doses of immunosuppressive therapy then allow donor T-cells to eradicate the remaining recipient HSCs and to induce the graft-versus-tumor effect.

[48] Because of their gentler conditioning regimens, these transplants are associated with a lower risk of transplant-related mortality, so allow patients who are considered too high-risk for conventional allogeneic HSCT to undergo potentially curative therapy for their disease.

The optimal conditioning strategy for each disease and recipient has not been fully established, but RIC can be used in elderly patients unfit for myeloablative regimens, for whom a higher risk of cancer relapse may be acceptable.

[43][45] After several weeks of growth in the bone marrow, expansion of HSCs and their progeny is sufficient to normalize the blood cell counts and reinitiate the immune system.

[54] Severe liver injury can result from hepatic veno-occlusive disease (VOD), newly termed sinusoidal obstruction syndrome (SOS).

In addition to inflammation, chronic GvHD may lead to the development of fibrosis, or scar tissue, similar to scleroderma; it may cause functional disability and require prolonged immunosuppressive therapy.

A transplant offers a chance for cure or long-term remission if the inherent complications of graft versus host disease, immunosuppressive treatments and the spectrum of opportunistic infections can be survived.

Patients who were successfully treated with HSCT and total body irradiation in childhood were found to have increased fat mass percentage, leading to significantly decreased exercise capacity in adulthood.

[68] The risks of a complication depend on patient characteristics, health care providers, and the apheresis procedure, and the colony-stimulating factor used (G-CSF).

The documented adverse effects of filgrastim include splenic rupture, acute respiratory distress syndrome, alveolar hemorrhage, and allergic reactions (usually experienced in first 30 minutes).

[70] There is no statistically significant evidence either for or against the hypothesis that myelodysplasia (MDS) or acute myeloid leukaemia (AML) can be induced by G-CSF in susceptible individuals.

[71] One study based on a survey of medical teams covered about 24,000 peripheral blood HSCT cases between 1993 and 2005, and found a serious cardiovascular adverse reaction rate of about one in 1,500.

This patient received regular blood transfusions, and an attempt was made to increase her leukocyte and platelet counts by intravenous bone marrow injection without unexpected reaction.

[73] Stem-cell transplantation was pioneered using bone marrow-derived stem cells by a team at the Fred Hutchinson Cancer Research Center from the 1950s through the 1970s led by E. Donnall Thomas, whose work was later recognized with a Nobel Prize in Physiology or Medicine.

In 2007, a team of doctors in Berlin, Germany, including Gero Hütter, performed a stem-cell transplant for leukemia patient Timothy Ray Brown, who was also HIV-positive.

[82] Levels of HIV-specific antibodies have also declined, leading to speculation that the patient may have been functionally cured of HIV, but scientists emphasise that this is an unusual case.

[83] Potentially fatal transplant complications (the "Berlin patient" developed graft-versus-host disease and leukoencephalopathy) mean that the procedure could not be performed in others with HIV, even if sufficient numbers of suitable donors were found.

After their transplant procedures, both were put on antiretroviral therapies, during which neither showed traces of HIV in their blood plasma and purified CD4+ T cells using a sensitive culture method (less than 3 copies/ml).

[87] Since McAllister's 1997 report on a patient with multiple sclerosis (MS) who received a bone-marrow transplant for chronic myelogenous leukemia (CML),[88] over 600 reports have been published describing HSCTs performed primarily for MS.[89] These have been shown to "reduce or eliminate ongoing clinical relapses, halt further progression, and reduce the burden of disability in some patients" who have aggressive, highly active MS, "in the absence of chronic treatment with disease-modifying agents".

[89] A randomized clinical trial including 110 patients showed that HSCT significantly prolonged time to disease progression compared to disease-modifying therapy.

[91] HSCT can also be used for treating selected, severe cases of other autoimmune neurological diseases such as neuromyelitis optica, chronic inflammatory demyelinating polyneuropathy, and myasthenia gravis.