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Bone marrow and stem cell transplants can come with significant side effects. Some of these side effects happen shortly after transplant. Others may develop months or even years later.
Your transplant team can help you manage these problems.
Problems that can happen soon after stem cell or bone marrow transplant include:
Many of these problems come from having your bone marrow wiped out by the conditioning treatment given just before the transplant (high doses of chemo or radiation to kill cancer and make room for new blood stem cells). You may also have side effects from the conditioning treatments themselves.
Your transplant team can help you cope with side effects. Some can be prevented, and most can be treated to help you feel better.
Always tell your transplant team about any problems you have or changes you notice.
Mucositis (inflammation or sores in the mouth) is a short-term side effect that can happen with chemo and radiation. It usually gets better within a few weeks after treatment, but it can make eating and drinking very painful.
Your transplant team can help you make a plan to manage your symptoms.
Chemotherapy drugs can cause severe nausea and vomiting. To try to prevent it, doctors often give anti-nausea medications before each dose of chemo. As much as possible, the goal is to prevent nausea and vomiting because it’s easier to prevent it than to stop it once it starts.
Anti-nausea medications should continue for as long as the chemo is likely to cause vomiting. This can be up to 7 to 10 days after the last chemo dose.
No single drug can prevent or control chemo-related nausea and vomiting 100% of the time. In many cases, two or more medications are used. Tell your transplant team how well the medicines are controlling your nausea and vomiting. If they aren’t working, they will need to be changed.
Infections that cause only mild symptoms in people with normal immune systems can be quite dangerous for you. This is because your white blood cells are the primary way your body fights off infection. Right after transplant, you don't have many white blood cells that are working well.
You may be given antibiotics to try to prevent infections until your blood counts reach a certain level.
Your new stem cells start making white blood cells (engraftment) within the first 6 weeks after your transplant. The risk of infections is lower after engraftment, but it still can happen.
Signs of infection include:
A fever is one of the first signs of infection. Sometimes it’s the only sign.
It's very important to contact your transplant team if you have a fever or any other signs of infection.
You will need to take your temperature by mouth every day or twice a day for a while. Your transplant team will let you know when to call them with your temperature.
If you get a fever, tests will be done to look for possible causes of the infection (chest x-rays, urine tests, and blood cultures) and antibiotics will be started.
Pneumocystis pneumonia (PCP): This is also called Pneumocystis jirovecii pneumonia. It is a serious fungal infection that can cause fever, cough, and serious breathing problems. The germ doesn’t harm people with normal immune systems, but it can affect people whose immune systems aren’t working correctly yet after transplant.
Cytomegalovirus (CMV): This is a common viral infection that many adults have or had in the past. Adults with healthy immune systems may not have any symptoms, but CMV can cause serious pneumonia in people who’ve had transplants. Pneumonia from CMV mainly happens to people who were already infected with CMV or whose donor had the virus.
Your transplant team checks your blood tests for CMV before transplant and gives you a special medication to keep it under control. If neither you nor your donor had CMV, the transplant team might follow special precautions to prevent this infection while you are in the hospital.
It can take 6 months to a year after transplant for your immune system to work as well as it should. It can take even longer if you have graft-versus-host disease (GVHD, see below).
You will be watched closely for signs of infection. Your transplant team will give you and your caregivers detailed information about the precautions you need to follow.
Avoid contact with:
Take extra care with food and meal prep:
After transplant, you are at risk for bleeding because the conditioning treatment destroys your body’s ability to make platelets. Platelets are the blood cells that help your blood clot.
Your platelet counts will be low for several weeks after transplant. During this time, you might notice easy bruising and bleeding, such as nosebleeds and bleeding gums.
While you wait for your transplanted stem cells to start working, your transplant team may have you follow special precautions to avoid injury and bleeding.
For more information on the transfusion process, see Blood Transfusion and Donation.
Pneumonitis is a type of inflammation (swelling) in lung tissue that’s most common in the first 100 days after transplant. But some lung problems can happen much later, even 2 or more years after transplant.
Unlike pneumonia, which is usually caused by germs, pneumonitis may be caused by radiation, graft-versus-host disease, or chemo. It can happen when the areas between the cells of your lungs (called interstitial spaces) get damaged.
If total body irradiation was given with chemo as part of the pre-transplant (conditioning) treatment, the risk of pneumonitis is higher and can be severe.
While you are in the hospital, you’ll get chest x-rays to watch for pneumonitis and pneumonia. Some doctors will do breathing tests every few months if you have graft-versus-host disease (see next section).
Report any shortness of breath or changes in your breathing to your transplant team right away.
There are many other types of lung and breathing problems that also need to be tested for and handled quickly.
Graft-versus-host disease (GVHD) happens when the donor cells from your transplant attack one or more of your organs. It can happen in allogeneic (allo) transplants when the immune cells from the donor see your body as foreign. (Your own immune system has mostly been destroyed by conditioning treatment and cannot fight back.)
The donor immune cells most often attack the skin, gastrointestinal (GI) tract, and liver. They sometimes attack other organs as well. This can change the way the organs work and increase the chance of infection.
GVHD reactions are very common and can range from mild to life-threatening. GVHD can be acute or chronic.
A person could have one, both, or neither type of GVHD.
Acute GVHD can happen 10 to 100 days after a transplant, though the average time is around 25 days.
Up to 47% of allo transplant recipients will develop acute GVHD. It’s less common in younger people and those with closer HLA matches between donor and recipient.
Because of recent improvements, acute GVHD happens less often and is less severe than it once was for people with mismatched donors. (See Finding a Stem Cell Donor for more on HLA matches.)
If acute GVHD happens, it is most often mild, mainly affecting the skin. But sometimes it can be more serious or even life-threatening.
Mild cases can often be treated with a steroid medication applied to the skin (topically) as an ointment, cream, or lotion, or with other skin treatments.
More serious cases of GVHD might need to be treated with a steroid medication taken as a pill or injected into a vein. If steroids aren’t effective, other medications that affect the immune system can be used.
Chronic GVHD can start anywhere from about 100 to 600 days after a stem cell transplant.
Up to half (50%) of allo transplant recipients will develop chronic GVHD.
Chronic GVHD is treated with medicines that suppress the immune system, much like those used for acute GVHD. These drugs can increase your risk of infection for as long as you take them. Most people with chronic GVHD can stop the immunosuppressive drugs after their symptoms improve.
A rash, burning, and redness of the skin on the upper chest, palms and soles is often the earliest sign of GVHD. The rash can spread over the entire body and is usually itchy and dry. In severe cases, the skin may blister and peel like a bad sunburn. A fever may also develop.
Other signs of GVHD of the skin include:
Signs of GVHD of the gut include:
Signs of GVHD of the liver include:
Doctors try to prevent acute GVHD by giving medications that suppress the immune system, such as steroids (glucocorticoids), methotrexate, cyclosporine, tacrolimus, and certain monoclonal antibodies.
A combination of some of these medications is given before acute GVHD starts and can help prevent serious GVHD. Still, mild GVHD will most likely happen after an allo transplant.
Researchers are looking for ways to prevent serious GVHD using different combinations of medications. One combination that studies show helps prevent serious GVHD is PTCy (post-transplant Cytoxan, tacrolimus, and mycophenolate).
The risk of acute GVHD can also be lowered by removing immune cells called T-cells from the donor stem cells before a transplant. But this can also increase the risk of viral infection, leukemia relapse, and graft failure (which is discussed later).
Researchers are looking at new ways to remove T-cells from donor grafts. This would reduce the severity of GVHD and still let the donor T-cells destroy any cancer cells left.
Sinusoidal obstructive syndrome (SOS), formerly called hepatic veno-occlusive disease (VOD), is a serious problem in which tiny veins and other blood vessels inside the liver become blocked.
SOS can happen in 5-15% of people with allo transplants. This amount varies depending on your risk factors and the conditioning regimen you receive.
SOS usually happens within about 3 weeks after transplant. It’s more common in older people who had liver problems before the transplant and in those with acute GVHD.
Signs of SOS start with:
SOS is life-threatening, so early diagnosis is very important.
Researchers continue to find ways to try to measure a person's chances of getting SOS so that treatment can start as soon as possible.
Grafts fail when your body doesn’t accept the new stem cells (the graft). If this happens, the new stem cells don’t go into your bone marrow and multiply like they should. Graft failure can lead to serious bleeding and/or infection.
Graft failure is more common if:
Graft failure is suspected in people whose counts don’t start going up within 3 to 4 weeks of a bone marrow or peripheral blood transplant, or within 7 weeks of a cord blood transplant. Still, it’s not very common.
It can be very upsetting when this happens, but you may be able to get treated with a second dose of stem cells, if they are available. Your transplant team will talk to you about other treatment options if needed.
You might have problems that show up months, years, or even decades after your stem cell treatment.
Possible long-term risks of stem cell transplant include:
Several things influence the type of problems that can happen after a transplant. This includes:
Other factors include the length and degree of immune system suppression, whether chronic graft-versus-host disease (GVHD) is present, and if so, how bad it is.
Long-term problems can also be caused by other medications, such as those that suppress your immune system after transplant. The medications used in transplants can harm your body’s organs, including your heart, lungs, kidneys, liver, bones/joints, and nervous system.
You will need careful follow-up with close monitoring and treatment of potential long-term organ problems. Some of these problems (like infertility) should be discussed before your transplant so you can prepare for them.
You will need routine check-ups for the rest of your life because it’s important to quickly find and manage long-term problems related to your treatment.
Tell your primary care doctor or transplant team right away if you notice any changes or problems. Physical exams by your local cancer care or transplant team might include:
These tests and others will help look for and keep a check on organ problems.
As transplant methods improve, more people are living longer and doctors are learning more about the long-term results of stem cell transplant.
Some transplant centers have a survivorship clinic to manage long-term problems. Researchers continue to look for better ways to care for survivors and offer the best possible quality of life.
The goal of a stem cell transplant in cancer is to prolong life and even cure the cancer in many cases. But sometimes the cancer comes back. This is called relapse or recurrence, depending on how long after a transplant it happens.
If cancer comes back, treatment options are often quite limited. A lot depends on your overall health at that point and whether the type of cancer you have responds well to medication treatment.
Treatment for people who are otherwise healthy and strong may include chemotherapy or targeted therapy.
Some people who’ve had allo transplants may be helped by getting white blood cells from the same donor to boost the graft-versus-cancer effect. This is called donor lymphocyte infusion. Sometimes a second transplant is possible.
Most of these treatments pose serious risks even to healthier people, so people who are frail, older, or have chronic health problems are often unable to have them. Other options may include palliative (comfort) care or a clinical trial.
It’s important to understand the expected outcome of any further treatment. Talk with your cancer care team about the purpose of the treatment and be sure you understand the benefits and risks before you decide.
There is also a chance of getting a second cancer after transplant. Studies show that people who have allo transplants are at higher risk of getting a second cancer than people who have a different type of stem cell transplant.
Second cancers that can happen after stem cell transplant include:
If they happen, these cancers tend to develop a few years or longer after the transplant.
Risk factors for getting a second cancer after stem cell transplant are being studied. These may include:
Successfully treating a first cancer gives a second cancer time (and the chance) to develop. This is true no matter what type of cancer you were treated for. Even without the high doses used for transplant, treatments like radiation and chemo can lead to a second cancer in the future.
Post-transplant lymphoproliferative disease (PTLD) is a cancer that can develop after an allo stem cell transplant. It is a type of lymphoma — an out-of-control growth of lymph cells.
PTLD after allo stem cell transplant is fairly rare.
PTLD is linked to B cells (a type of white blood cell that is part of the immune system) and the presence of Epstein-Barr virus (EBV).
T-cells normally help rid the body of cells that contain viruses. When the T-cells aren’t working well, EBV-infected B-lymphocytes (a type of white blood cell) can grow and multiply.
Most people are infected with EBV at some time during their lives, but the infection is controlled by a healthy immune system. Pre-transplant treatment weakens the immune system, allowing the EBV infection to get out of control. This can lead to PTLD.
PTLD is life-threatening. It may show up as lymph node swelling, fever, and chills.
Rituximab is considered 1st line treatment for PTLD. It’s often treated by cutting back on immunosuppressant drugs to let a person’s immune system fight back. Other treatments include chemo, radiation, immunotherapy, and CAR-T.
Even though PTLD doesn’t often happen after transplant, it’s more likely to occur with less well-matched donors and when strong suppression of the immune system is needed. Studies are being done to identify risk factors for PTLD and look for ways to prevent it in people who have had a transplant and are at risk.
Most people who have stem cell transplants become infertile (unable to have children).
This is not caused by the transplant itself, but by the high doses of chemo and/or radiation therapy. These treatments affect both normal and abnormal cells and often damage reproductive organs.
Your cancer care or transplant team may be able to tell you if your treatment is likely to cause infertility.
If having children is important to you, or if you think it might be important in the future, talk to your cancer care or transplant team. They can refer you to a fertility specialist and discuss ways to protect your fertility before treatment.
For more information on having children after cancer treatment, see Fertility Problems.
After chemo or radiation, some women may find their menstrual periods become irregular or stop completely.
Even if your periods stop, you may still be able to get pregnant. The medications used in transplants can harm an unborn child, so it’s important to use birth control before and after a transplant.
The medications used during transplant can also damage sperm. To avoid starting a pregnancy, men should use birth control during the transplant process. Your transplant team can tell you how long you need to be careful.
Transplants may cause temporary or permanent infertility for men as well. Fertility returns in some men, but the timing is unpredictable. Men might consider storing their sperm before having a transplant.
Your transplant team will tell you how long after transplant you need to avoid starting a pregnancy.
You might go through feelings of distress, anxiety, depression, joy, or anger. Adjusting emotionally after a stem cell transplant can be hard because of the length of time you feel ill and isolated from others.
You might feel like you are on an emotional roller coaster during this time. Support and encouragement from family, friends, and the transplant team are very important to get you through the challenges after transplant.
Reach out to support groups, social workers, or counselors for help.
Developed by the American Cancer Society medical and editorial content team with medical review and contribution by the American Society of Clinical Oncology (ASCO).
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Last Revised: July 10, 2025
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