Methotrexate for inflammatory bowel disease

Inflammatory bowel disease (IBD) is a term used to describe medical conditions such as:

These are long-term conditions involving inflammation of the gut.

Methotrexate is used to treat a variety of medical conditions including IBD, particularly Crohn’s disease and less commonly ulcerative colitis. It can be used on its own or in combination with other medicines such as infliximab or adalimumab.

They work by suppressing the body’s immune system to treat inflammation.

These drugs act slowly, so it may be up to 3 months before benefits are seen.

Most people will be treated with methotrexate for several years. 

Unlicensed medicine

Methotrexate is not licensed to treat IBD use but it is considered a safe and effective treatment. Read more about unlicensed medicines

Before you start the medicine

You will need a few blood tests to make sure it's safe for you to start taking the medicine. These may include tests to check:

  • your blood count
  • tuberculosis (TB)
  • liver and kidney function
  • hepatitis B 
  • hepatitis C
  • Epstein-Barr virus, which causes glandular fever
  • HIV
  • chickenpox

Before you start taking methotrexate, we strongly recommend you have the vaccine against strains of pneumonia. Your GP can arrange this for you.

You should also let your doctor know about all the medicines you take. This should include anything prescribed for you and any medicines you buy from a shop or pharmacy (including herbal and homeopathic).

It is important to make sure you are not pregnant before starting treatment. If you are unsure, you will be required to take a pregnancy test.

How to take the medicine

Methotrexate is taken once a week in a single dose on the same day each week. 

It can be taken either by tablets or by injection. Sometimes people start with injections before moving to tablets, and sometimes it’s the other way around.

Tablets should be swallowed whole with a glass of water while sitting upright or standing. Take them after food and do not crush or chew them.

It is important that all medicines are kept out of the reach of children. 

Methotrexate comes in 2.5mg (milligram) tablets (usually a pale yellow round-shaped tablet) and 10mg tablets (usually pale yellow oval-shaped tablet). 

Guy's and St Thomas' only supplies 2.5mg tablets. 

Make sure that your GP prescribes 2.5mg tablets. Always check when you receive your prescription as a higher dose can cause serious side effects. 

Check with your doctor or pharmacist as soon as possible if you think that you have been given the wrong dose.

Methotrexate injections can be given into muscle (intra-muscular) or usually under the skin (subcutaneous). 

In most cases you will be trained to inject the methotrexate yourself.

We prescribe folic acid tablets to take with methotrexate. Folic acid is a vitamin that helps reduce some of the possible side effects. 

Take the folic acid on a different day as your weekly methotrexate dose so that you get the full benefit from your treatment.

Methotrexate and folic acid tablets can look similar. Keep them in their individual original containers to avoid confusion.

If you forget to take a dose

If you forget to take your methotrexate, you can take it the following day or 2 days after. 

Do not take the dose if you are 3 or more days late without talking to the IBD team first.

Do not double your dose if you have forgotten.

Try not to forget any doses. Methotrexate works slowly and if you regularly forget the medicine, you will have a lower level in your blood. This can make it less effective.

If you forget to take your folic acid you can take it when you remember, any day of the week, except the day of your methotrexate dose.

Getting a repeat prescription

After your hospital specialist has started you on methotrexate, they'll advise your GP what dose to prescribe.

Your first prescriptions will be given to you by the hospital until your GP has agreed to prescribe them to you. If your GP does not agree to prescribe your methotrexate, your prescriptions will continue to be supplied from our hospital

If any changes to the dose are needed then the hospital will tell your GP.

Regular blood tests

When you first start methotrexate you will need regular blood tests. Blood tests will be checked at the hospital 2, 4, 8 and 12 weeks after starting the medicine.

If your blood tests are stable after 3 months of treatment then you should continue to have them checked every 3 months with your GP.

Monitoring blood tests are essential. If these are not done your prescription may be withheld until you have your blood test.

Our specialist doctors and pharmacists monitor you to assess for side effects or abnormalities in your blood tests. You should expect to have regular appointments or phone calls from them.

We give you a booklet for you to record your blood results in. Keep this up to date and take it to appointments with your hospital doctor, GP, pharmacist, dentist, and other healthcare providers. Your pharmacist may want to look at the booklet before they supply your methotrexate, so please take it with you to the pharmacy.

Taking methotrexate with other medicines

Methotrexate can interact with other medicines. You should always check with your doctor or pharmacist before starting any new medicines, in particular antibiotics such as co-trimoxazole and trimethoprim along with non-steroidal anti-inflammatory medications like ibuprofen.

Avoid ‘live’ vaccines when you are taking methotrexate, and for at least 3 months after stopping it. If you are considering having vaccinations check with your doctor or pharmacist first. If anyone in your family or household is due to have a live vaccine, check with your IBD team whether you need to take any special precautions.

You should arrange a flu jab every year with your GP. You should also have a pneumonia vaccination every 5 years, while being treated with methotrexate.

Side effects

Everyone responds differently to the medicine but possible side effects include:

  • feeling sick (nausea), especially at the start of treatment
  • diarrhoea (runny poo)
  • fatigue or drowsiness

Methotrexate increases the skin’s sensitivity to the sun and so increases the risk of certain types of skin cancer. Wear protective clothing and use a high sun protection factor (SPF 50) sun cream.


Methotrexate works by suppressing the immune system. This means you might be more likely to get an infection. 

Call a GP, our team or 111 straight away if you:

  • notice any unexplained signs of bruising or bleeding
  • have a high temperature (fever)
  • notice jaundice (yellowing of the eyes or skin)
  • have severe upper stomach pain
  • notice a rash after starting the medicine
  • have swollen face, hands and feet
  • have trouble breathing or swallowing
  • have shortness of breath, chest pain or a persistent cough

Go straight to the emergency department (A&E) if you feel very unwell.

Serious allergic reaction

It's possible to have a serious allergic reaction.

Call 999 or go to A&E now if:

  • you get a skin rash that may include itchy, red, swollen, blistered or peeling skin
  • you're wheezing
  • you get tightness in the chest or throat
  • you have trouble breathing or talking
  • your mouth, face, lips, tongue or throat start swelling

You could be having a serious allergic reaction and may need immediate treatment in hospital.

More serious side effects 

More serious side effects will be monitored on your regular blood tests. In some cases, we may decide to stop the medicine. Most of these are rare and affect between 1 in 1,000 and 1 in 10,000 cases. 

  • The medicine can suppress your bone marrow which reduces the number of red cells, white cells and platelets produced. 
  • Abnormal liver function tests can happen in about 1 in 20 people.  
  • Abnormal kidney function. 
  • Allergic reactions.

If you are concerned about any symptoms, contact the IBD Advice line by emailing [email protected]

Pregnancy and breastfeeding

Methotrexate may seriously harm your baby when taken during pregnancy.

Do not take methotrexate if you are pregnant and wait a minimum of 3 months after finishing your treatment before trying to become pregnant. Do not breast feed while on methotrexate.

If you become pregnant while on treatment, stop taking your methotrexate immediately and let the IBD team and your GP know.

Use a reliable form of contraception whilst taking methotrexate. 

It's important you tell us if you are pregnant or planning on getting pregnant so that we can review all of your medicines and monitor you more closely.

Drinking alcohol

We recommend you keep well within the national recommended limits of alcohol (maximum of 14 units per week).

14 units is about the same as 6 pints of average-strength beer or 10 small glasses of lower-strength wine.

Any amount of alcohol can damage the liver, especially if you have an underlying condition. Depending on the state of your liver, your clinician may ask you to avoid alcohol completely.

Useful information

Crohn’s and Colitis UK has more information about IBD.

Resource number: 4467/VER2
Date published: May 2022
Review date: May 2025

Trusted Information Creator. Patient Information Forum

Contact us

If you have any questions or concerns about your treatment and condition:

Email the IBD advice line: [email protected]

Please include your name, hospital number, contact details and details of your enquiry. We will respond 9am to 5pm Monday to Friday.

If you are concerned outside these hours, please contact your GP or call NHS 111.

If you have any questions or concerns about methotrexate, email the IBD pharmacy team: [email protected]

You can also call the gastroenterology department during office hours on 020 7188 2499 or 020 7188 1222

Do you have any comments or concerns about your care?

Contact our Patient Advice and Liaison Service (PALS)

Is this health information page useful?