A bone marrow transplant can offer the possibility of long-term disease control or cure for people with certain blood cancers and serious blood disorders. However, it is also an intensive treatment, and complications can occur during the transplant process, in the months that follow, or even years later.
The risks are not the same for everyone. They depend on the disease being treated, the patient's age and general health, the conditioning treatment used before transplant, whether the stem cells come from the patient or a donor, and how quickly the immune and blood-forming systems recover.
If you are considering treatment, the Bone Marrow Transplant process involves careful assessment and monitoring before, during and after transplantation to identify and manage these risks as early as possible.

*AI-generated image - for illustration only. Clinical accuracy is not guaranteed.
Why can a bone marrow transplant cause complications?
A transplant is more than an infusion of healthy stem cells. Before the transplant, patients often receive high-dose chemotherapy, sometimes with radiation, to destroy abnormal cells and make room for the new stem cells.
This treatment can temporarily suppress the bone marrow and immune system. As a result, the body may have too few white blood cells to fight infections, too few platelets to control bleeding, and too few red blood cells to carry oxygen efficiently.
In an allogeneic transplant, where the stem cells come from another person, there is an additional challenge: the donor's immune cells may recognize the recipient's tissues as foreign. This can lead to graft-versus-host disease, one of the most important complications after transplant.
The risks can change as recovery progresses
Not every complication occurs at the same time. Some are most likely during the period when blood counts are very low, while others may develop months or years after transplantation.
During the early transplant period
The first few weeks can be physically demanding because blood counts and immunity are suppressed. Common problems during this period can include:

*AI-generated image - for illustration only. Clinical accuracy is not guaranteed.
- Fatigue and weakness
- Nausea and vomiting
- Loss of appetite
- Mouth and throat sores
- Diarrhoea
- Hair loss
- Low blood counts
- Infections
- Bleeding or bruising
Some of these effects are related primarily to the conditioning treatment rather than the stem cells themselves. Supportive treatment, transfusions, medicines and careful monitoring are often used during this period.
Infections are an important concern
After transplantation, the immune system needs time to rebuild. During this period, bacteria, viruses and fungi can cause serious infections. Infections can occur at different stages of recovery. The type of infection a patient is vulnerable to can change as different parts of the immune system recover.
This is why transplant recipients may need infection-prevention medicines, monitoring, vaccination planning and precautions around food and exposure to infectious illnesses.
A fever or other possible sign of infection after transplant should be taken seriously because an infection can worsen quickly when the immune system is weakened.
Low blood counts can cause bleeding and anaemia
Conditioning treatment can temporarily reduce the production of blood cells. Low platelet levels can increase the risk of bruising and bleeding, while low red blood cell levels can contribute to tiredness, weakness and shortness of breath.
In some patients, platelet or red blood cell transfusions are needed until the new blood-forming system becomes established. Bleeding can occur in different parts of the body and, in severe cases, can become life-threatening. The risk is particularly important when platelet counts are very low or when other transplant complications are present.
Graft-versus-host disease: a risk unique to donor transplants
Graft-versus-host disease (GVHD) occurs after an allogeneic transplant when immune cells from the donor recognize the recipient's tissues as foreign and attack them. It can affect several organs, particularly the:
- Skin
- Liver
- Digestive system
- Mouth and eyes
- Lungs and other tissues in chronic disease
GVHD can be acute, chronic, or have features of both. Acute GVHD commonly affects the skin, liver and gastrointestinal tract, while chronic GVHD can involve multiple organs and may persist for a prolonged period.
The risk of GVHD is one reason donor selection and immune-suppressing medicines are such important parts of allogeneic transplantation. It is also important to understand that GVHD is not simply a sign that the transplant has failed. Donor immune cells can also contribute to the graft-versus-tumour or graft-versus-leukemia effect, in which they help attack remaining abnormal cells. The challenge is controlling harmful immune reactions without losing the potential anti-cancer benefit.
What happens if the new stem cells do not establish properly?
After the stem cells are infused, they need to travel to the bone marrow and begin producing new blood cells. This process is called engraftment.
In some patients, the graft may fail to establish adequately. Graft failure can result in prolonged low blood counts and can become a serious or life-threatening complication.
The risk can be influenced by the underlying disease, conditioning regimen, donor and graft characteristics, infections and other factors. Patients are therefore monitored closely for evidence that the transplanted cells are successfully establishing themselves.
Other complications that may occur during recovery
Transplant-related complications can affect more than the blood and immune systems. Depending on the type of transplant and treatment received, doctors may monitor for:
- Liver complications: including sinusoidal obstruction syndrome, sometimes called veno-occlusive disease.
- Kidney problems: which can result from medicines, infections, dehydration or other transplant-related factors.
- Lung complications: including infections, inflammation and treatment-related lung injury.
- Heart complications: which may be associated with previous or transplant-related treatments.
- Thrombotic complications: including blood clots and transplant-associated microangiopathy.
- Neurological complications: which can have infectious, medication-related, metabolic or immune causes.
These complications are not inevitable. Their likelihood varies significantly between patients, which is why transplant teams perform regular blood tests, imaging and organ-function assessments when indicated.
Some risks appear later
Recovery does not necessarily end when blood counts return to normal. Some transplant-related effects can develop months or years later. Possible long-term complications include:
- Persistent or chronic GVHD
- Fertility problems
- Hormonal or endocrine problems
- Cataracts and other eye problems
- Bone and muscle weakness
- Heart, lung, kidney or liver problems
- Secondary cancers
- Persistent immune-system abnormalities
- Ongoing fatigue or reduced physical functioning
Not everyone experiences these problems. Their likelihood depends on factors such as previous chemotherapy or radiation, transplant type, age, GVHD, other medical conditions and the treatments used before and after transplantation.
Can a bone marrow transplant affect fertility?
Yes. Some chemotherapy and radiation treatments used before transplantation can damage the reproductive system and may affect fertility in both men and women.
The risk depends on the conditioning regimen, age, sex and other individual factors. Because fertility problems can be permanent, fertility preservation should be discussed before conditioning treatment begins whenever possible. Depending on the situation, options may include sperm or egg preservation and other fertility-preservation approaches.
What increases the risk of complications?
There is no single factor that determines whether someone will develop complications. Risk can be influenced by several characteristics, including:
- Age and general health
- The underlying disease and its status before transplant
- Previous chemotherapy or radiation
- Conditioning intensity
- Autologous versus allogeneic transplantation
- Degree of donor-recipient compatibility
- Stem cell source
- Infections before or after transplant
- Development of GVHD
- Other existing medical conditions
Modern transplant programs use risk assessment before treatment to determine whether the expected benefits of transplantation justify its potential complications.
How are transplant complications detected?
Close monitoring is one of the most important parts of transplant care. Patients may have frequent blood tests and physical examinations, particularly during the early recovery period.

*AI-generated image - for illustration only. Clinical accuracy is not guaranteed.
Depending on the patient's condition, doctors may monitor blood counts, kidney and liver function, infections, disease status, donor-cell engraftment and signs of GVHD. Additional tests such as imaging, lung-function testing or specialist assessments may be performed when symptoms or risk factors indicate a need.
Long-term follow-up is also important because some complications are delayed. Regular surveillance allows problems to be identified and treated before they become more difficult to manage.
Which symptoms should never be ignored?
After a bone marrow transplant, the transplant team should be contacted promptly if concerning symptoms develop. Depending on the stage of recovery, these may include:
- Fever or chills
- New or worsening shortness of breath
- Unusual bleeding or extensive bruising
- Persistent vomiting or diarrhoea
- A new or rapidly spreading skin rash
- Yellowing of the skin or eyes
- Severe abdominal pain
- Confusion, seizures or new neurological symptoms
- Sudden deterioration in general condition
These symptoms can have many causes, and not every symptom means a serious complication has developed. However, early assessment is particularly important after transplantation because infection, GVHD and other complications can progress rapidly.
Does every bone marrow transplant carry the same risks?
No. The risk profile can be quite different between patients. An autologous transplant, in which a patient's own stem cells are returned, does not carry the same GVHD risk as an allogeneic transplant. An allogeneic transplant introduces donor immune cells and therefore creates additional risks, including GVHD and complications related to immune recovery.
Similarly, a patient's conditioning treatment, underlying disease and general health can substantially change the likelihood of particular complications. This is why transplant risks are best discussed in the context of the specific transplant being proposed rather than using a single overall complication rate.
Can these complications be prevented?
Not every complication can be prevented, but many risks can be reduced or detected early. Examples include careful donor selection, infection-prevention strategies, medicines to reduce GVHD, blood-product support, monitoring of organ function, appropriate nutrition and physical activity, vaccination planning and long-term screening.
The goal is not simply to treat complications after they occur. Modern transplant care focuses heavily on anticipating risks and intervening early.
The Bottom Line
Bone marrow transplantation can be a potentially life-changing treatment, but it is also a complex procedure with short- and long-term risks. Early complications may include infections, low blood counts, bleeding, mouth sores, gastrointestinal problems and treatment-related organ injury. In allogeneic transplantation, graft-versus-host disease and graft failure are additional major concerns.
Long-term complications can include chronic GVHD, fertility problems, organ damage, bone and muscle weakness, cataracts and, in some patients, secondary cancers. However, these complications do not occur in everyone, and their risk varies according to the disease, transplant type, conditioning treatment, donor characteristics and the patient's overall health.
For this reason, transplant care continues well beyond the day the stem cells are infused. Careful monitoring during the early recovery period and long-term follow-up help doctors identify complications early and manage them as effectively as possible.