Methotrexate for IBD

Points to remember

  • Methotrexate is an effective medication used to treat inflammatory bowel disease (IBD) and is generally taken once a week.
  • Regular blood test monitoring ensures side effects can be detected and addressed promptly.
  • Methotrexate can increase the risk of spontaneous abortion and birth defects when taken by women. Please discuss any plans for pregnancy, or fathering a pregnancy, if you plan to start or are on methotrexate.

Key points 

  • Methotrexate is a slow acting medication and it may take one to three months to start working.
  • Methotrexate is sometimes used by itself and sometimes used with other medications to increase its effectiveness.
  • Methotrexate is taken as a single dose, once a week, on the same day each week either as a tablet or injection.
  • Folic acid (vitamin B9) may also be prescribed to you to reduce possible side effects caused by methotrexate.
  • Side effects from methotrexate may include nausea, vomiting, loss of appetite, fatigue, mouth ulcers and rashes.

Why have I been prescribed methotrexate and how does it work?

Methotrexate is a medication that is used to treat IBD (which includes Crohn’s disease and ulcerative colitis). The immune system is important for fighting infections but in IBD, there is an imbalance in the immune system. This imbalance can cause inflammation and damage to the bowel. Methotrexate reduces and controls inflammation in your bowel by dampening down the immune system. It may help to reduce the need for steroid medication. If you respond well to methotrexate you should be able to keep taking it for some years. It can also be used in combination with other IBD medications to improve overall effectiveness of your treatment. In general, methotrexate is slow acting. It may take 1-3 months before you start noticing benefits.

At much higher doses than those used in IBD, methotrexate can be used to treat some types of cancer.

What checks do I need to have before starting methotrexate?

Some patients with kidney, liver, lung or bone marrow problems, may not be able to take methotrexate, so before you start treatment, the IBD team will request blood tests including your kidney function, full blood count and liver function.

You will also be screened to check you are up to date with your vaccinations and for certain infections before starting treatment.

Methotrexate can interact with some medications. Therefore, the IBD team will ask you about any other regular medications, vitamins, herbal supplements, antibiotics or over the counter medications, to make sure they are safe to take together.

How do I take methotrexate?

Methotrexate is taken as a single dose, ONCE A WEEK, on the same day each week. It may occasionally be prescribed by your doctor to be taken as a split-dose twice a week, but never more often.

If you forget to take your methotrexate on your normal day, you can take it 1-2 days later. You should not take your methotrexate 3 or more days late. Just take your regular dose on the usual day next week. DO NOT double up the dose. Contact your IBD team if unsure.

There are two different forms of methotrexate, tablet or syringe.


The tablets should be swallowed with a full glass of water, after food. Do not crush or chew them. Methotrexate tablets come in 2 different strengths, 2.5 mg and 10 mg. It is important that you check your dose of methotrexate and the strength of tablets supplied.

Subcutaneous (under the skin) injection

Oral absorption of methotrexate can, in some people, be unpredictable or not well tolerated, so many doctors will prescribe subcutaneous methotrexate. A subcutaneous injection is an injection into the fat, usually on the abdomen or thigh. Your IBD team will train you on how to handle and inject the methotrexate, or you may elect to have your injections administered once a week by your GP. Prefilled syringes of methotrexate are also available.

Why have I also been prescribed folic acid?

Taking folic acid (vitamin B9) can help you tolerate methotrexate and reduce some of the possible side effects. You may be told to take folic acid once a week or on days other than the day you take your methotrexate depending on the regimen your doctor uses.

What checks will I need while I am taking methotrexate?

Regular blood tests are very important as methotrexate can supress normal bone marrow function and cause liver complications. Regular blood tests can pick up abnormalities in the blood that may not produce symptoms straight away. Your IBD team will discuss and provide a blood test monitoring schedule. When you have had a blood test it is important that you contact the IBD team for the results and further dosing instructions.

Fertility, pregnancy and breastfeeding

Women who are trying to conceive or are pregnant should not take methotrexate as it can increase the risk of spontaneous abortion and birth defects. Women of childbearing age on methotrexate should take reliable contraception. Women planning pregnancy are advised to see their IBD team and ideally stop methotrexate 6 months prior to conception.

The effects on sperm are less well documented and should be discussed with your IBD team. It is currently recommended that males use reliable contraception and stop methotrexate 3 months prior to conception.

Methotrexate passes into the breastmilk and can affect the baby’s immune system and growth. Avoid breastfeeding while taking methotrexate.

What are the possible side effects of methotrexate?

All medicines can cause side effects, but not everyone experiences them. You will be monitored for side effects by your IBD team. Side effects from methotrexate may include nausea, vomiting, loss of appetite, fatigue, mouth ulcers and rashes. Methotrexate can increase the risk of infections, such as the common cold, and less commonly, more serious infections such as shingles. Please contact your doctor if you have a fever or feel unwell. Less common side effects include lung and liver problems. There is some evidence that methotrexate may slightly increase the risk of lymphomas (cancer of the lymph glands).

Please be aware when reading product information for methotrexate that information (especially about side effects) is provided for both the low once-a-week (anti-inflammatory) doses used in IBD and high (chemotherapy) doses used for some cancers.

What can I do to keep myself healthy on methotrexate?

  • Avoid close contact with people with transmissible infections. Tell your doctor if you have come in contact with anyone who has an infectious condition such as chicken pox, shingles, whooping cough or measles.
  • Alcohol and methotrexate can interact and may affect your liver. Your doctor may advise you to reduce alcohol consumption while on methotrexate.
  • You should have the flu vaccine every year, and the COVID-19, pneumonia, and human papillomavirus (HPV) vaccines according to the recommended schedule. You should not have live vaccinations while taking methotrexate, and for some time after stopping it. Please refer to the Vaccinations and IBD information sheet for further information.
  • Women should have regular cervical screening tests as recommended by your GP.
  • Always check with your IBD team before starting new medications to avoid unwanted interactions.

Contact the IBD team or your GP if you have an infection or persistent fever.

This information leaflet has been designed to provide you with some important information about methotrexate. This information is general and not intended to replace specific advice from your doctor or any other health professional. For further information please speak to your pharmacist, doctor or IBD nurse.


This resource was developed in 2021 by the GESA IBD Patient Information Materials Working Group