Early Recovery Period - Short Term Side Effects

After your bone marrow or stem cell transplant, your medical team will monitor you for potential complications and respond quickly if problems arise.

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It will take a few weeks for the transplanted stem cells to begin producing healthy blood cells. This is called engraftment.


The two-to-three-week period after the transplant is a critical time. The conditioning regimen will have destroyed your stem cells, temporarily crippling your immune system and your ability to make red blood cells, white blood cells and platelets.

  • If you were transplanted with bone marrow or peripheral blood stem cells, you can expect engraftment to take two-to-three weeks.
  • If you were transplanted with cord blood, engraftment can take longer - typically three-to-five weeks

Daily blood samples will be taken to determine whether the stem cells have begun producing new blood cells.

Once your stem cells are producing a sufficient number of healthy blood cells, you will be discharged from the hospital or outpatient center, provided no other complications have developed.

Short-Term Side Effects 

The chemotherapy and total body irradiation (TBI) you are given during the conditioning regimen are toxic to normal tissues and organs as well as diseased cells. During the first few weeks after transplant several side effects can occur. 

Anxiety about side effects is norma. It helps to remember that most short-term side effects of transplant are temporary and completely reversible.


Until the healthy blood stem cells engraft, you will be at risk of developing an infection. The risk is less if you had a reduced intensity transplant. 
Precautions will be taken to minimize your exposure to viruses and bacteria.
  • You will be given antibiotics, as needed, to prevent and fight infection.
  • Medical personnel will wash their hands with antiseptic soap and may wear gloves and/or a mask while visiting you.

In addition, you may need to:

  • wear a mask when leaving the clinic or the hospital room 
  • avoid foods that may contain harmful bacteria 
  • avoid young children, people who are sick and certain pets until your immune system is functioning normally

Platelets and Red Blood Cells

The chemotherapy or radiation may also destroy the platelets in your blood which help blood clot. You may receive platelet transfusions during this time to prevent excessive bleeding.

You may also need blood transfusions to replace the red blood cells destroyed by the conditioning regimen until your blood counts recover.

Nausea, Vomiting, and Diarrhea 

Nausea, vomiting and diarrhea are common after transplant, but can usually be controlled with medication.

Drugs called antiemetics are used to control nausea. Antiemetics can cause temporary side effects such as:

  • anxiety 
  • drowsiness 
  • restlessness 
  • muscle tightness 
  • •uncontrolled eye movement 
  • shakiness

These reactions can be frightening to observe but are usually less serious than they appear. Lowering the dosage of the antiemetic or administering an antihistamine usually reduces or eliminates the symptoms.

Diarrhea following the conditioning regimen is also common. Antidiarrheal drugs such as Lomotil® may be used to sedate the nerves in the gastrointestinal area, slowing down muscle contractions and the diarrhea.

Mouth and Throat Sores 

High-dose chemotherapy and TBI target rapidly dividing cells like cancer cells. However, some normal cells also divide rapidly, such as those that line the mouth, throat and gut. 

Mouth and throat sores are common after transplant and typically appear four-to-eight days following the conditioning regimen.

  • Topical anesthetics such as Dyclone® or drugs such as morphine are used to relieve this discomfort.
  • Your transplant team may prescribe other medications to reduce the severity and duration of mouth and throat sores.
  • Frequently brushing your teeth and gums with a soft brush or sponge, and rinsing with a saline solution helps prevent mouth infections. 
  • There are also rinses that can help reduce the discomfort caused by mouth sores.

Mouth sores can make eating difficult. You may be fed intravenously until the discomfort subsides and your stomach is able to absorb sufficient nutrients.

Antacid medication may be needed to counteract stomach irritation.

Learn more about managing eating problems after transplant.

Hair Loss

The conditioning regimen usually causes temporary hair loss (alopecia). Hair loss changes your appearance and, for some, can be very distressing.

  • Some patients prefer to shave their head or cut their hair very short before hair loss begins.
  • Scarves, hats or wigs can be used until the hair grows back. 
  • Hair normally grows back within three-to-six months

Sometimes the amount of curl or thickness of the new hair will differ from your hair pre-transplant. In rare cases, hair loss may be permanent.

Skin Rash

Skin rash is common with conditioning regimens that include TBI, busulfan, etoposide, carmustine or thiotepa.

Less often, dark spots appear on the skin. This is called hyperpigmentation and is most often seen in patients with a darker skin tone. The spots usually fade in one-to-three months.

Watch a video about protecting your skin and hair after transplant

Bladder Irritation 

Bladder irritation occasionally occurs following the conditioning regimen, particularly those that include cyclophosphamide or ifosfamide. It may cause bloody or painful urination.

To prevent or treat the problem your transplant team may:

  • increase the flow of intravenous fluids
  • use a catheter to irrigate your bladder
  • give you a drug called MESNA®

Liver Problems 

Temporary liver damage occasionally occurs following the conditioning regimen. It is usually both mild and completely reversible.

You may experience:

  • jaundice (yellowing of the skin)
  • significant weight gain due to fluid retention
  • abnormal blood levels of liver enzymes and bilirubin (a pigment produced during the breakup of red blood cells)

Resting the liver and avoiding medications that aggravate the condition are the usual treatments until the liver heals itself.

Sinusoidal obstruction syndrome (SOS), previously called venoocclusive disease (VOD), is a complication that occurs in up to 15% of transplant patients.

  • The blood vessels that carry blood through the liver become swollen and blocked.
  • Without a supply of blood, the liver cannot remove toxins, drugs and other waste products from the bloodstream.
  • Fluids build up in the liver causing swelling and tenderness.• The kidneys may retain excess water and salt, causing swelling in the legs, arms and abdomen.

In severe cases, excess fluid in the abdominal cavity puts pressure on the lungs making it difficult to breathe. Toxins that are not processed out of the blood by the liver may affect how the brain functions causing confusion (although confusion is also a symptom of other, less serious problems).

A drug called defibrotide is available to help treat this complication.


Breathing irregularities occasionally occur following the conditioning regimen. You may have difficulty taking a deep breath, develop a new cough or have new findings on a chest X-ray that prompt the doctors to prescribe new medications or order new tests.

Occasionally, patients develop infectious pneumonia or inflammation in the lungs. Extra fluid may build up in the lungs. If the problem is severe, the patient may be admitted to the intensive care unit (ICU). In most cases, however, the injury to the lungs is temporary.


Mild, temporary heartbeat irregularities (arrhythmia) or rapid heartbeat (tachycardia) can occur following the conditioning regimen, particularly after those that include cyclophosphamide or carmustine. Severe heart problems are rare. 


Confusion is an occasional side effect of the conditioning regimen or of drugs used to control side effects. Confusion can be frightening for both you and your loved ones.

The problem is usually temporary and reversible and may be managed by changing the dosage or type of drug that is causing the problem.

Muscle Spasms/Cramping after Transplant

Muscle spasms or cramping are common after transplant and are usually caused by an imbalance in electrolytes — minerals found in the body such as potassium, magnesium and calcium. The problem can often be resolved by taking supplements to replace the minerals that were lost.

Ask your doctor to prescribe the supplement since not all products containing these minerals are absorbed equally well by the body.

If there is no electrolyte imbalance, vitamin E or quinine may help.


During the early recovery period, expect to feel very fatigued. Moderate exercise can help you regain your strength and stamina.

At some transplant centers, patients are encouraged to walk the hallways to build up their strength. Other programs have stationary bikes patients can ride to improve stamina. Even a little bit of daily exercise is helpful for your recovery. Consult with your healthcare team about the appropriate amount of exercise for you.

Acute Graft-versus-Host Disease (GVHD)

Graft-versus-Host Disease is a common complication following a transplant using donor cells. GVHD is not an issue for patients who had a transplant using their own stem cells.

There are two forms of graft-versus-host disease: acute and chronic. Patients who develop acute GVHD usually do so during the first three months after transplant.

Learn more about graft-versus-host disease.

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Next page: Returning home after transplant

Updated June 2024