HSCT, or hematopoietic stem cell transplant, is a medical procedure that replaces damaged or diseased blood-forming cells with healthy ones. Sometimes called a bone marrow transplant, it works by infusing healthy stem cells into a patient’s bloodstream, where they travel to the bone marrow and begin producing new blood cells. It’s used to treat blood cancers like leukemia and lymphoma, as well as a growing list of autoimmune diseases including multiple sclerosis.
How HSCT Works
Your bone marrow contains stem cells that produce every type of blood cell your body needs: red blood cells, white blood cells, and platelets. When these stem cells become cancerous or when your immune system turns against your own body, HSCT essentially hits the reset button. The treatment wipes out the faulty cells and replaces them with healthy ones that can rebuild a functioning blood and immune system from scratch.
The process follows a clear sequence. First, healthy stem cells are collected, either from the patient themselves or from a donor. Next, the patient undergoes intensive chemotherapy (and sometimes full-body radiation) to destroy the diseased bone marrow. Then the collected stem cells are infused into the bloodstream through an IV, much like a blood transfusion. Those cells naturally migrate to the bone marrow, settle in, and start producing new blood cells. This settling-in process is called engraftment, and it marks the beginning of recovery.
Autologous vs. Allogeneic Transplants
There are two main types of HSCT, and the choice between them depends on what’s being treated, how old the patient is, and whether a suitable donor is available.
Autologous transplants use the patient’s own stem cells. Before the intensive chemotherapy begins, stem cells are collected from the patient’s blood, filtered, and stored. After the conditioning treatment destroys the diseased marrow, those stored cells are infused back. This type is most commonly used for lymphoma, multiple myeloma, and autoimmune diseases. Because the cells come from the patient’s own body, there’s no risk of the new immune system attacking the patient’s tissues.
Allogeneic transplants use stem cells from a donor, typically a sibling or matched unrelated donor. The donor receives injections for four to five days beforehand that coax stem cells out of their bone marrow and into the bloodstream, where they can be collected through a filtering process called apheresis. This type is used primarily for leukemias and other bone marrow disorders. One advantage of allogeneic transplants is that the donor immune cells can recognize and attack remaining cancer cells, a phenomenon called the graft-versus-malignancy effect. The tradeoff is a higher risk of serious complications.
Conditions Treated With HSCT
HSCT is most established as a treatment for blood cancers. Allogeneic transplants are the standard approach for many forms of leukemia and myelodysplastic syndromes, while autologous transplants are widely used for lymphoma and multiple myeloma.
The use of HSCT for autoimmune diseases has expanded significantly. According to 2025 recommendations from the European Society for Blood and Marrow Transplantation (EBMT), multiple sclerosis and systemic sclerosis (scleroderma) are now the two standard autoimmune indications for autologous HSCT. There is also supporting evidence for its use in carefully selected patients with Crohn’s disease, lupus, neuromyelitis optica, myasthenia gravis, stiff person syndrome, certain types of vasculitis, and refractory celiac disease.
For solid tumors, HSCT plays a limited role. It may be considered for germ cell tumors and, in highly selected cases, for Ewing’s sarcoma, soft tissue sarcomas, and medulloblastoma. But for most solid cancers, it remains experimental or is not recommended.
What the Treatment Process Looks Like
Stem Cell Collection
If you’re having an autologous transplant, your stem cells will be collected before conditioning begins. You’ll receive injections that push stem cells from your bone marrow into your bloodstream. Then you’ll sit for several hours connected to an apheresis machine, which draws blood, filters out the stem cells, and returns the rest. For allogeneic transplants, the donor goes through this same process.
Conditioning
This is the most physically demanding phase. You’ll receive high-dose chemotherapy, sometimes combined with total body radiation, over several days. The goal is to destroy the diseased cells in your bone marrow and suppress your immune system enough that it won’t reject the new stem cells. The intensity of conditioning varies. Some patients receive full-intensity regimens, while others, particularly older patients or those with other health issues, may receive reduced-intensity conditioning that’s less toxic but still effective.
Infusion and Engraftment
The stem cell infusion itself is relatively straightforward, similar to receiving a blood transfusion through an IV line. What follows is a vulnerable waiting period. Your old immune system has been wiped out and the new one hasn’t yet taken hold. During this time you’re at high risk for infections and will need close monitoring. Engraftment, when the new stem cells begin producing blood cells, typically happens within the first two to three weeks.
Hospital Stay and Recovery Timeline
If you undergo an inpatient transplant, expect to be in the hospital for roughly 12 to 28 days, depending on your treatment plan. Most patients are ready for discharge 11 to 16 days after the stem cell infusion. But going home doesn’t mean recovery is over.
The first 100 days after transplant are considered the most critical period. Your immune system is still rebuilding, and you’ll need to take precautions against infection: avoiding crowds, washing hands frequently, and possibly wearing a mask. You’ll have regular blood draws and clinic visits to monitor your counts and watch for complications. Full immune reconstitution takes much longer, often 12 months or more for autologous transplants and up to two years for allogeneic transplants. During this time, you’ll gradually return to normal activities, though energy levels and stamina can take months to fully recover.
Risks and Complications
HSCT is one of the most intensive treatments in medicine, and it carries real risks. The conditioning phase causes side effects common to high-dose chemotherapy: nausea, fatigue, mouth sores, hair loss, and a severely weakened immune system. Infections are a major concern during the weeks when blood counts are at their lowest.
The most significant complication specific to allogeneic transplants is graft-versus-host disease (GvHD), where the donor’s immune cells attack the patient’s own tissues. In a study of patients over 60, acute GvHD occurred in about 73% of cases, though only around 10% were severe. Chronic GvHD developed in about 31% of patients, with a median onset around 7.5 months after transplant. Severe GvHD is associated with substantially higher rates of serious infections, including bacterial sepsis and viral reactivation. GvHD can affect the skin, liver, gut, and other organs, and managing it often requires long-term immunosuppressive medication.
Treatment-related mortality, meaning death from the procedure itself rather than from the underlying disease, varies considerably by transplant type. Autologous transplants are much safer, with mortality rates around 2 to 3%. Allogeneic transplants carry higher risk, with non-relapse mortality reported at roughly 9 to 17% in recent studies for matched donors, and higher still for mismatched donors or older patients.
How Effective Is HSCT for Multiple Sclerosis?
Because many people searching for HSCT are specifically interested in its use for MS, the results are worth looking at separately. A long-term outcomes study published in JAMA Neurology found that about 46% of MS patients who received autologous HSCT remained free of disability progression at five years. That figure reflects all types of MS combined. Patients with relapsing-remitting MS (the most common form) and those treated earlier in their disease course tend to do better.
HSCT for MS works by wiping out the immune cells that are attacking the nervous system and regrowing a new immune system that, ideally, no longer targets the brain and spinal cord. It is not a guaranteed cure, and some patients do relapse or continue to progress. But for patients who have failed standard disease-modifying therapies, it represents one of the most aggressive options available.
Who Is Eligible
Not everyone is a candidate for HSCT. Selection depends on the specific disease, how advanced it is, the patient’s overall fitness, and whether the potential benefits outweigh the serious risks of the procedure.
For MS, typical eligibility criteria include having a disability score of 8 or below on the 10-point EDSS scale (meaning the patient is not yet bedbound) and a general functional status above 70%, indicating the ability to care for oneself. Patients with relapsing-remitting MS who continue to have relapses despite medication are the strongest candidates. Those with advanced progressive MS, where damage has already accumulated over many years, are less likely to benefit because HSCT stops immune-driven inflammation but cannot repair nerve damage that’s already occurred.
For cancers, eligibility depends on the specific diagnosis, the stage of disease, whether the cancer responds to chemotherapy, and the patient’s age and organ function. Allogeneic transplants require finding a donor whose immune markers closely match the patient’s, which can be a limiting factor. A matched sibling is the ideal donor, but registries of unrelated donors and the use of partially matched family members have expanded access significantly.