IBD Testing and Treatment in Pregnancy

What if you flare during pregnancy?

One-third of women who were in remission before pregnancy develop a flare during pregnancy. One common reason for a flare is stopping medications, so if you are on stable meds, please do not discontinue them.

If you flare even though you are on your medications, call your gastroenterologist so they can rule out infections. IBD puts women at greater risk for Clostridium difficile (C. difficile) infection, so you will need to have a stool test to check for this, and if it is positive, you will need to take antibiotics to clear up the infection. If it turns out that you do not have C. difficile, you may need an adjustment in your IBD medications.

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Medical procedures during pregnancy


X-rays should generally be avoided during pregnancy due to the risk of radiation. However, there may be situations where they are needed during an emergency. When required, these tests can be done, and the radiation risk is actually very low with newer technologies.

Magnetic Resonance Imaging (MRI)

Getting an MRI is considered safe after the first trimester. However, you should make sure to tell the technician if you are pregnant as they may want to avoid the contrast (gadolinium) which is a chemical sometimes given during a MRI using IV.


Routine endoscopy (a long tube with a tiny camera at the end that is put into your digestive system to help diagnose or assess how your IBD is doing), is generally not recommended during pregnancy. However, if there is a concern, endoscopy can be done, and there should be no issues with the bowel prep having any effect on the fetus. Also, a safe sedation will be used.

Do not delay having your colonoscopy if you need one. A healthy mom means a healthy baby. 

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IBD medications during pregnancy

Women living with Crohn’s disease or colitis may be concerned about the effects of IBD medications on their developing fetus. However, most IBD medications are safe during this time, and it is more important to try to keep your disease in remission. 


Some women who have an ileal pouch (J-pouch, S-pouch, or W-pouch) may develop an infection that requires antibiotics. Physicians generally refrain from prescribing the antibiotic ciprofloxacin during pregnancy due to possible effects on the fetus.

5-Aminosalicylic acid (5-ASA)

This class of drugs is generally very safe. Also, when using as a suppository, it does not get to the bloodstream, and is of no concern during pregnancy. If you choose to breastfeed, you can rest assured they are safe when breastfeeding also.

One exception is if you are taking a type of 5-ASA that contains an ingredient called dibutyl phthalate (DBP), which may have some potential to cause birth defects.

If you are in the preconception stage and you are taking a medication containing DBP, your doctor may switch to a different medication.

However, if you are already pregnant in your first trimester and your IBD is well controlled with a medication containing DBP, switching medications could lead to an IBD flare which can be harmful during pregnancy. The decision to switch medications depends on the patient and what their healthcare team thinks.


Prednisone is a commonly used steroid medication used to treatment Crohn's and colitis. We tend to use this class of drug more as a rescue agent if the IBD is not under optimal control, and not as a maintenance (long-term) therapy.

During pregnancy, corticosteroids may increase the risk of maternal blood pressure or gestational diabetes, which is a major concern for the fetus. If you normally take corticosteroids, talk to your gastroenterologist about other options to keep your disease in remission.

Methotrexate and tofacitinib

These two oral medications are not safe during pregnancy. Examples of these drugs include Trexall and Xeljanz. 

Speak to your gastroenterologist at least three months before pregnancy to discuss phasing out these drugs and replacing them with alternate medications. You should also consult a high-risk OBGYN as soon as you can.


Azathioprine (Imuran) or mercaptopurine (Purinethol, Purixan) are two types of immunosuppressant drugs used to treat Crohn's disease and ulcerative colitis. These medications are considered safe during pregnancy. They are also safe when breastfeeding.

Biologics and biosimilars

One class of IBD medications that people tend to be most concerned about is biotherapies, including biologics and biosimilars. However, biologics have been found to be safe during pregnancy.

Biologics or biosimilars do not need to be stopped during pregnancy, and they can safely be continued to the last trimester.

Biologics are large molecules, too large to cross the placenta barrier in the first trimester in significant amounts, and thus they do not cause birth defects. They do readily cross the placenta barrier in the second and third trimesters, but there is no evidence that biologics need to be stopped during this time.

There is no significant risk of severe infection with biologics during pregnancy.

Some women are concerned about giving their babies vaccinations if they were exposed to biologics during pregnancy. Babies exposed to biologics can receive all non-live vaccines (pertussis, polio). The timing of live vaccines, such as MMR (measles, mumps, rubella) and rotavirus, needs to be discussed on a case-by-case basis with your healthcare provider.

For IBD patients that are already taking biologic medication, it is not recommended to switch to a biosimilar during pregnancy or breastfeeding. Learn more about these medication in our Biotherapies section

Rectal therapies (suppositories/enemas)

These are therapies that work by inserting the medications through the rectum. There is no evidence that they cause preterm birth. The rectum is often the hardest area to treat when you have IBD, so if you are given a suppository, it will provide extra help to that spot if it is inflamed.

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