Having an FMT by colonoscopy

Faecal microbiota transplantation (FMT)

Faecal microbiota transplantation (FMT) is for treating diarrhoea, caused by a bacteria called Clostridioides difficile (C diff) and symptoms caused by ulcerative colitis. 

The FMT is given either as an inpatient (if you are staying on a ward) or as a day case. It will be done on the endoscopy unit at St Thomas' hospital.

FMT by colonoscopy needs special preparation and is usually done with sedation. 

The procedure takes 30 to 40 minutes. An endoscopy nurse will be with you the whole time.

Preparing for your first FMT by colonoscopy

If you treat your ulcerative colitis with enemas or suppositories, you'll be asked to stop this 2 weeks before your first FMT. You can carry on with all your other medicine as usual.

You will also be asked to take a laxative the day before the procedure. This is medicine that speeds up your bowel movements.

You will need to follow a high-fibre diet for 3 days before taking the laxative. We'll give you more information about this in your pre-assessment appointment.

We'll prescribe you loperamide to take just before you have the colonoscopy. This is an anti-diarrhoea medicine and helps the FMT to work.

Preparing for FMT for C diff infection by colonoscopy

If you are still taking antibiotics to treat your C diff infection (CDI), for example fidaxomicin or vancomycin, you will be asked to stop these 48 hours before your colonoscopy. 

You will also be asked to take a laxative (medicine that speeds bowel movement) beforehand.

You will need to drink more fluids on the day before the procedure. You should aim to drink a glass of water every hour.

Full details will be given to you by your doctor.


You should have had the chance to talk about any medicines you are taking with your doctor or nurse before your procedure.

If you are taking antiplatelet or anticoagulants medicines to prevent blood clots (such as aspirin or clopidogrel, warfarin, rivaroxiban or dabigatran), tell your doctor or nurse before the date of your procedure.

You should also tell them if you are taking sedatives, chronic pain medicines, or medicines for diabetes.

You should be able to take all of your medicines as usual, unless you have been told otherwise by the doctor or endoscopy nurse.

When you arrive

When you arrive at the endoscopy unit, give your name to the receptionist or nurse.

You will be asked to sit in the waiting area before being seen by an endoscopy nurse, who will ask you about your medical history. Tell the nurse if you have had any reactions or allergies to other tests or procedures in the past.

We ask you to remove all of your clothing and change into a gown. You might want to bring your dressing gown and slippers with you.

During FMT by colonoscopy

Once you are ready, you will be taken to the second waiting area, called the ‘sub wait area’.

In the procedure room, your doctor will explain more about the procedure and answer any questions you might have.

You will be given loperadmide, an anti-diarrhoea medicine, to help the FMT to work.

FMT is usually done with sedation. If you are having sedation, a small plastic tube (cannula) will be inserted into your arm. 

You will be asked to lie down on your left-hand side on a couch, with your knees bent. A small, thin, tube called an endoscope will be put into your lower bowel through your bottom (anus).

The transplant liquid will be passed down the endoscope during the procedure. This might make you feel bloated, and you might feel like you need to go to the toilet, or pass wind. This is perfectly normal and is nothing to be embarrassed about.

Pain during an FMT

You might feel some discomfort, particularly when the endoscope is first put in.

You can choose to have:

  • sedation, medicine that makes you sleepy and relaxed, but does not put you to sleep
  • an injection of painkillers
  • Entonox (gas and air) 

Sometimes the doctor or nurse will press gently on your stomach or change your position to help the endoscope be put in.

After FMT by colonoscopy

After the procedure, you will be taken to the recovery area.

If you are not staying on a ward and do not have any other appointments on the day of your FMT, you can leave hospital the same day. However, we do recommend that you wait until after you have had a poo (opened your bowels).

If you have not had sedation you will be taken to the discharge area and you can leave the hospital straight after your procedure.

If you have sedation, you will need to rest quietly until the sedative has worn off, which usually takes a couple of hours. The nurse will check your blood pressure and pulse, and offer you some tea and biscuits. 

You must have someone to take you home and stay with you for 24 hours after your FMT. They should come with you to your appointment or be contactable by phone when you are ready to leave.

If you do not have someone to take you home, your procedure will be cancelled. 

If you cannot arrange for someone to collect you, contact your team to talk about other arrangements.

Even though you might feel well, the sedation lasts longer than you might think. In the first 24 hours after the procedure, you should not:

  • drive a car, or ride a bicycle
  • operate machinery
  • do anything that needs skill or judgement
  • drink alcohol
  • take sleeping tablets
  • go to work
  • make any important decisions, such as signing contracts or legal documents

After FMT by colonoscopy

You should rest at home after your procedure. You can eat and drink normally and should be able to carry out your usual activities 24 hours after the procedure.

After the procedure, you are very likely to have loose bowel motions (diarrhoea) and feel a little bloated. The gut often takes a few days to begin to get better.

You should notice how often your poo slows down, and that your poo is less runny. After a week, you should be having poo which is almost normal. During this time, you may have some stomach cramps or feel sick.

Go to your nearest emergency department (A&E) if:

  • you have severe tummy (abdominal) pain
  • you have a high temperature (fever)
  • you pass large amounts of blood after the procedure

Resource number 3975/VER3
Published date: February 2023
Review date: February 2026

Contact us

If you have any questions or concerns about your faecal microbiota transplantation (FMT) treatment at our hospitals, please contact the endoscopy department.

Phone: 020 7188 7188 extension 54059, Monday to Friday, 8am to 6pm

Please note that you cannot self-refer for this treatment.

Referrals are only accepted from local gastroenterology clinicians.

We cannot answer enquiries unless you are a patient at our hospitals.

Do you have any comments or concerns about your care?

Contact our Patient Advice and Liaison Service (PALS)

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