Fertility, Pregnancy and IBD

IBD is most commonly diagnosed for the first time between the ages of 15 and 35. This means a lot of people are diagnosed around the time they are thinking of starting a family. It is only natural then to be concerned about how your disease may affect your chances of getting pregnant and if you can deliver a healthy baby. 

The good news is that most women with IBD are able to have children and raise a family just like everyone else. However, in certain situations like if you’re having a flare or have had certain surgeries, it can make pregnancy more difficult. 

Even without having IBD, there is a lot to think about when deciding to have a baby, so it’s important to learn about what you can do to keep both you and your child healthy before, during and after pregnancy. 

Watch our information forum hosted in May 2021 where you will hear from Gastroenterologist Dr Emma Flanagan, who specialises in IBD and pregnancy.

Fertility & IBD 

Key points 

  • Fertility is not directly affected by Crohn’s and colitis but certain treatments can interfere with fertility. 
  • Surgery in the pelvic area, like J pouch surgery or a permanent ostomy can increase infertility in women. 
  • Fertility in both men and women can be decreased during a flare so maintaining remission is important when trying to get pregnant. 
  • Some medications can interfere with infertility but by switching medicines fertility can be restored after some time. 

The overall fertility rate for women with Crohn’s and ulcerative colitis is similar to women without IBD. However, it’s important to keep in mind that certain surgeries or medical treatments for IBD may impact fertility. So, if you or your partner with IBD plans on becoming pregnant in the future, it’s a good idea to talk with a doctor who understands the special care required during this important time in your life. 

Surgery and fertility 

Pelvic surgery, especially the J pouch surgery or a permanent ostomy with removal of the rectum, can decrease fertility. This is due to scarring around the fallopian tubes and ovaries that happens with pelvic surgery. Although older studies say that J pouch surgery can increase the risk of infertility by three times, newer studies show that fertility rates are much improved with laparoscopic (keyhole) surgery. 

Surgical procedures that remove the rectum (for example, proctocolectomy with ileostomy or ileal pouch anal anastomosis surgery) can on rare occasions reduce men’s ability to achieve an adequate erection or ejaculation. Newer surgical techniques, however, that remove the rectum have significantly reduced the risk of this complication. 

Surgery can sometimes be postponed if a couple wishes to start or complete their family, but it is always important to strike a balance between the benefits and risks of postponing or proceeding with an operation. Each IBD case is unique, and treatments are highly specialised, so it is important to have any operation discussed with the IBD team and done by a specialist colorectal surgeon.  

Inflammation and fertility 

Fertility may be reduced in patients with active Crohn’s disease due to decreased ovarian reserve. Anti-Müllerian hormone (AMH) levels have recently been shown to be a good indicator of ovarian reserve and can be a marker of fertility among women of reproductive age. Several studies have shown that women with active Crohn’s disease, especially disease affecting the colon, have significantly decreased AMH levels. Similar studies have not been conducted in women with UC so this remains unknown. 

Severe active disease or a lack of adequate nutrition can also reduce sperm count, which usually returns to normal once the IBD is brought under control and health and nutrition are restored.  

Medication and fertility 

Treatment with corticosteroids can cause temporary irregularities in the menstrual cycle as well as amenorrhoea (the complete absence of periods) sometimes for months at a time. This returns to normal when corticosteroid dosages are reduced or discontinued. 

Sulfasalazine, which is one of the aminosalicylate or 5-ASA-containing medications, is known to have a negative effect on sperm. Within two months of starting sulfasalazine treatment, sperm count decreases, the presence of abnormal spermatozoa increases, and sperm motility is decreased. All of these changes are dose-related and are reversible. This issue can be avoided by would-be fathers by switching medications at least three months before attempting to conceive, by which time their sperm will have returned to normal. 

Methotrexate can also lower sperm count but this returns to normal after discontinuing the medication. Men are advised to discontinue methotrexate three months before attempting to conceive. 

Choosing not to have children 

Although not a cause of infertility, voluntary childlessness is more common among people with IBD. People with IBD often choose to have fewer or no children for a number of reasons, including: 

  • fear of worsening disease during pregnancy 
  • concern of passing IBD on to their offspring 
  • concern of disease recurrence because of pregnancy 
  • concern regarding increased stress due to a child 
  • fear of not being able to care for a child 

IVF (in vitro fertilisation) 

IVF is a helpful option for women with IBD who are unable to conceive. Since IVF bypasses the fallopian tubes, any scarring due to prior surgery should not affect the results. 

In a large study of women who underwent IVF, the ability to have a live birth was reduced in those women with Crohn’s disease and ulcerative colitis compared to the general population of women undergoing IVF. Women with Crohn’s disease who had surgery had a further reduced chance of a live birth compared to women with Crohn’s disease who did not have surgery. However, surgery did not affect the rate of live births for women with ulcerative colitis. 

Heredity & IBD 

Key points 

  • A family history of IBD can increase the risk of children developing the disease at some point in their lives. 
  • There is a significantly higher chance of a child not developing IBD even if a parent has been diagnosed with the disease. 
  • Because the causes of IBD are not yet understood there are no ways to reduce the risk of a child developing IBD. 

Will I pass IBD on to my children? 

If you or a relative has Crohn’s disease or ulcerative colitis, you might wonder what role family history plays in IBD, especially when it comes to having children of your own.  

If you take 10,000 people from the general population, about two people per year have a chance of developing IBD. If you also include a family history of IBD, that chance increases by 4 to 8 times. 

It’s important to keep in mind that you will not be passing on IBD but the increased risk of developing the disease. This risk depends on which family member has IBD and is 5-8% higher if one parent has the disease. If both parents have the disease, the chance of a child developing IBD increases to a third. 

This means that a child has a 92% chance of not having IBD if one parent has it, and a 65% chance of not having it, even if both parents are affected. The risk is not considered large enough to discourage anyone with IBD from starting or adding to a family. 

Can I do anything to reduce the risk of my child developing IBD? 

The causes of developing IBD are still being researched and the reasons why IBD runs in families are not fully understood. Genetics are only one factor involved in the likelihood of a child developing the disease. Environment and the microbiome also have a part to play which is still being explored by researchers. 

Since the cause of IBD is unknown, there are no sure ways to decrease the likelihood of passing on the risk of developing the disease to your child. What you can do is become as knowledgeable about the disease as you can so you can be a strong pillar of support if your child is diagnosed with IBD. 

Nutrition for a healthy pregnancy 

Key points 

  • Caring for your nutrition and diet is important for people with IBD planning to have a baby because the disease often affects nutrient levels. 
  • Folic acid, vitamin D and iron will often need supplementation before or during an IBD pregnancy. 
  • If you’re planning on getting pregnant, an accredited dietitian can help tailor a diet to suit you and your baby’s needs. 

When planning for pregnancy and during pregnancy, good nutrition will help you have a healthy baby. Thinking about nutrition is especially important for people with IBD because the disease can interfere with the absorption of nutrients. The disease can also limit what you can eat and reduce your appetite. 

With these additional factors in play, talking with your health care professional can set you on the right path even before you conceive. This will mean you’ll have time to spot any nutritional deficiencies and plan a diet that includes everything you need for yourself and your baby. 

What nutrients should I look out for? 

Folic Acid and Folate: Folic acid is important to have a healthy baby and protects your baby from neural tube (brain, spine and spinal cord) birth defects like spina bifida. Some IBD medications like methotrexate or sulfasalazine, can increase the risk of folic acid deficiency. 

You should begin taking 600-800 micrograms (the dosage found in most prenatal vitamins) of folate daily as soon as you are contemplating pregnancy and throughout your pregnancy. If you have a folate deficiency or are on sulfasalazine, you should take a higher supplementation of folate, around 1000-2000 micrograms (1-2 milligrams) per day as recommended by your doctor. 

Vitamin D: Low vitamin D levels are common in people with IBD and can decrease fertility and increase the risk of miscarriage. 

Prescription-strength doses of Vitamin D, typically 50,000 International Units weekly for 8-12 weeks, may be recommended depending on your level of deficiency. It’s important to know what kind of Vitamin D you are using to supplement your diet, because Vitamin D3 may absorb more efficiently than Vitamin D2 does. 

Iron: It is common for all women, not just women with IBD, to need iron supplementation during pregnancy. This need often increases for women with IBD because of bleeding in the gut which leads to iron loss. 

It can be difficult for people with IBD to take iron supplements because they often lead to abdominal pain and constipation. But there are other ways to take iron either in a drink or intravenously. You can always talk about what is best for you and your baby with your doctor. 

What should I eat during my pregnancy? 

Any supplements you are on should be supporting a nutritional diet that has good sources of protein, iron, calcium and folic acid. Depending on your current diet you may want to make some changes to make sure there is a good intake of these important nutrients. 

Protein: Red meat, poultry, fish, tofu, eggs, lentils, quinoa 

Iron: Red meat, poultry, fish, spinach, leady greens & beans (iron will absorb better if vitamin C rich foods like oranges are eaten at the same time. Avoid eating plant-based iron foods at the same time as dairy since calcium can decrease iron absorption.) 

Calcium: Milk, yoghurt, cheese, calcium-fortified cereals and juices 

Folic acid: Fortified cereal, bread, legumes, leafy greens, citrus fruits 

Will my pregnancy be affected if I am underweight? 
In general, women will need to increase their calorie intake by 200-300 calories a day during the first two trimesters and by 500 calories during the third. 

Women who are underweight or have active disease may need to increase this by 10% to 20%. Being underweight during pregnancy has been connected with an increased risk of underweight or preterm babies. Finding help from a dietitian with knowledge of IBD can really help to develop a diet that addresses all your needs for a healthy pregnancy. 

Which foods should I avoid during my pregnancy? 

Pregnant women can be more easily affected by serious infections like listeria and salmonella which are caused by food. To reduce your chances of getting these infections try to avoid eating: 

  • Raw or undercooked meat, eggs and seafood (sushi often has one of these) 
  • Unpasteurised milk, by itself or in foods  
  • Cold meats (e.g. chorizo, prosciutto, etc…), smoked seafood and pâtés (meat pastes) 

IBD and medication during pregnancy 

Key points 

  • Active disease is the main cause of pregnancy complications so it is important to try and stay in remission during pregnancy. 
  • Most IBD medications are safe for your baby but there are some that must be avoided before and during pregnancy. 
  • Have a talk with your gastroenterologist 3-6 months before you’re planning to have a child so that you can feel confident in the medications you are using during your pregnancy. 

The single most important thing you can do to have a healthy pregnancy and delivering a healthy baby is to have your IBD under control, ideally before you attempt to become pregnant and also throughout the pregnancy. That’s why it is important to be on top of the medication you are using and talk with your doctor about your plans to have a child 3-6 months ahead of time. 

Women with IBD are at higher risk for spontaneous abortions and other pregnancy complications compared to those without IBD. So it’s best to have close follow-up with your doctor and specialists during this time. Before making any changes to your IBD medications, make sure that you, your obstetrician and your doctor are all on the same page about what treatment plan is best for you.  

Is it safe to keep using my medication during pregnancy? 

Many people are afraid to take medication while pregnant, and this is understandable. This fear may be increased by the Therapeutic Goods Administration (TGA) classification of medication safety in pregnancy, which is often based on animal studies or theoretical concerns.  

Electronic prescribing programs used by GPs may show warnings when IBD medications such as mesalazine are prescribed. However, these pop-up warnings are based on outdated data that do not take into consideration the negative effect of disease activity during pregnancy.  

The guidelines that IBD doctors use to care for pregnant patients are those from expert agencies, such as ECCO (European Crohn’s and Colitis Organisation), which classifies medications based on studies with real patients, and expert experience with these drugs. It has been found that many IBD drugs are safer in real-world experience than their ‘official’ ratings. Therefore, it is usually not necessary to change the medicines you take for IBD before you try to conceive. 

There are a lot of different types of medication for IBD so it can be overwhelming to figure out what the best treatment is for you and your baby. That’s why it is important to discuss your medication plan with your doctor. 

Most medicines that treat IBD are safe for your baby but there are a few that should be avoided before, during and after your pregnancy if breastfeeding. 

Aminosalicylates (5-ASA): Commonly used for mild to moderate ulcerative colitis 5-ASAs do not affect the immune system. They are safe to continue during pregnancy — as well as during breastfeeding — to treat symptoms and maintain remission.  

One exception may be Asacol HD (mesalamine), which specifically contains a chemical in the coating of the tablet, not the drug itself, that has been linked to birth defects in rabbits. If you are taking Asacol HD and are planning a pregnancy or are pregnant, talk to your doctor about switching to another form.  

Another, sulfasalazine, is known to interfere with the metabolism of folic acid, which is essential for normal foetal development. All women who are pregnant or who are trying to become pregnant should take supplemental folic acid to reduce the risk of neural tube defects (e.g., spina bifida) in their unborn child, and this is especially true for women taking sulfasalazine. 

Allopurinol: Some people need to take this medication with azathioprine or 6-mercaptopurine. There is not yet enough information from studies to recommend continuing use of allopurinol during pregnancy, and it may be unsafe to continue taking it, so it is best to discuss this with your doctor before conception. Your doctor may stop the allopurinol and either find another medication to treat your IBD during pregnancy or continue use of azathioprine without allopurinol. 

Antibiotics: Many doctors use antibiotics to treat infections, pouchitis and some fistulas. Avoiding ciprofloxacin is recommended, but instead using short courses of metronidazole (Flagyl) and Augmentin when necessary. For women who develop C. difficile infection, vancomycin is recommended. 

Corticosteroids: Budesonide is used for less serious symptoms that require prednisone. It is unclear if budesonide is safer than prednisone during pregnancy. During pregnancy, if your IBD is severe enough to use steroids, your doctor will generally prescribe prednisone as it’s stronger and controls active inflammation faster. Your doctor should try to use the least amount of steroids possible to control the disease, as active IBD is the main risk factor for complications, not the drug itself. 

Infants who are being breastfed while the mother is taking moderate or high doses of corticosteroids should be monitored by a paediatrician. 


Azathioprine/6-MP: In high doses azathioprine is used to treat cancer and is associated with a high risk for birth defects in women using these during pregnancy. However, this is not the case with the dosage used to treat IBD. In fact, their use is associated with better outcomes during pregnancy.  

Methotrexate and thalidomide: Both increase the risk of birth defects when taken by either men or women. These drugs should therefore be stopped 6 months before conceiving, after discussion with your IBD treatment team, and a safer alternative should be prescribed. All women taking methotrexate or thalidomide should use a reliable form of contraception. If you are taking either of these drugs and experience an unplanned pregnancy, you should stop using the drug and see an obstetrician and your IBD specialist for immediate counselling. 

Mycophenolate mofetil: May cause miscarriages or birth defects if used during pregnancy and cannot be used while breastfeeding either. If you’re being treated with this drug, you’ll usually be advised to stop taking it at least 6 weeks before conception. Men and women should use reliable contraception during treatment and for at least 90 days after stopping the medication. 


Anti-TNFs: Are all considered safe during pregnancy. In fact, many doctors may start a woman on an anti-TNF during pregnancy rather than use steroids.  Research on infants exposed to anti-TNF therapies during pregnancy does not suggest any increased risk for birth defects or developmental abnormalities. 

Anti-TNF drug levels in newborn infants take a few months to clear from the blood if a mother receives any medications after the beginning of the third trimester. Therefore, it’s recommended that infants do not receive any vaccines that use live viruses like rotavirus. Use is also fine during breastfeeding as it does not appear any of these agents are secreted into milk. 

Vedolizumab (Entyvio) and ustekinumab (Stelara): Are newer medications with limited data about their safety in pregnancy. If you are using either of these medications, please discuss them with your gastroenterologist before conceiving. Women who conceive while using these drugs may elect to continue, after discussion with their gastroenterologist about alternative options, but should have close monitoring of the baby. 

JAK kinase inhibitors (tofacitinib): Limited human data. Consider other options, particularly in first trimester. 

Anti-diarrhoeal agents: Should always be used with caution. While occasional or low-dose use might be necessary from time to time, it is important that anti-diarrhoeal medications are avoided just before and during labour. 

Enemas, foams, suppositories: Although there is some absorption into the bloodstream of the active ingredients of rectal formulations of IBD medications, the amount absorbed is rarely enough to cause any problems and need not be an issue, given that oral preparations of aminosalicylates and corticosteroids are considered safe to use during pregnancy. 

Monitoring and management of IBD during pregnancy 

Key points 

  • Staying in regular contact with your IBD team before, during and after pregnancy will keep you on top of any unexpected developments. 
  • Surgery is always risky for the wellbeing of mother and child and should be avoided if possible, during pregnancy. 
  • Some testing procedures are not safe for your foetus like CT scans and full colonoscopies. 

You should check in with your IBD treating team at least once per trimester (every three months) during pregnancy and 6 weeks after birth, in addition to your usual obstetric care.  

Flares during the pregnancy may further heighten the risk for premature deliveries and low birth weights at a time when testing and treatment options may be more limited. Therefore, it’s important to remain vigilant about controlling IBD inflammation from conception to birth.  

Pregnancy itself does not increase disease activity or cause flares but stress caused by pregnancy can worsen disease symptoms. 

Is it safe to have surgery during pregnancy? 

If needed, yes it is, but routine surgery which could have been performed beforehand should not be done. This is one of the reasons why you should plan ahead and aim to spend as much time in remission as possible. 

Any type of surgery during pregnancy is risky for the wellbeing of the mother and the foetus and, wherever possible, should be avoided until after delivery. Fortunately, there is rarely a need for IBD-related surgery during pregnancy. 

In some cases, though, putting surgery off until after delivery might present a significant risk to the mother. And although any type of abdominal surgery presents risks to the developing foetus, there are also cases where the risk to the foetus would be greater if surgery was put off. As always, the risks involved with surgery need to be weighed against the danger of ongoing disease activity and the lack of response to medical treatment. 

Is it safe to have diagnostic procedures during pregnancy? 

In general, investigations involving x-rays and radiation, including CT scans, should be avoided by pregnant women, especially during the first trimester (first three months).  

Blood test results and symptoms can be affected by pregnancy, so alternative tests, such as measurement of faecal calprotectin and an intestinal ultrasound, may be recommended to check for disease activity. 

Tests should only be done when the need to investigate the mother’s health outweighs the risk to the foetus, as when there is a disease flare-up that is not responding as expected to treatment. In this instance, MRI (without use of a contrast agent) can be considered after Week 20. Endoscopy can be used during pregnancy if the disease is severe, with light sedation and close monitoring, and is safe for the baby.  

 Regardless of the method of diagnostic procedure, supreme care must be taken to shield the developing foetus from any radiation. 

If diagnostic procedures are required during pregnancy to manage disease or plan a change in treatment, the following procedures are considered safe to perform: 

  • abdominal ultrasound 
  • sigmoidoscopy 
  • rectal biopsy 
  • gastroscopy 
  • limited colonoscopy (a full colonoscopy is technically more demanding in the later stages of pregnancy and could present a greater risk) 
  • MRI scans. 

Delivery with IBD 

Key points 

  • Most women with IBD will have a normal vaginal delivery. 
  • Complications with active disease or surgery may lead doctors to recommend you have a caesarean delivery. 
  • Research has shown that both vaginal and caesarean deliveries have no effect on your IBD. 

You’re nearly there and about to welcome a new bundle of joy. It’s perfectly normal to have some fear as the big day approaches and if you are worried about anything, talk with your doctor so you can feel as prepared as possible. Knowing what delivery options are before you can help make you feel more in control. 

Will having IBD affect how I deliver my baby? 

Most women with IBD can and do have a normal vaginal delivery. This method is the first choice unless there are childbirth reasons to perform a caesarean section (C-section). 

Women with Crohn’s disease complicated by perianal fistulae and abscesses involving the anal and genital areas are generally advised not to have an episiotomy (an incision to widen the birth canal) because of possible difficulties with the healing process. In these cases, caesarean delivery would be recommended. 

Caesarean delivery is often recommended by doctors for women who have had J pouch surgery for ulcerative colitis, in order to preserve the function of the pouch and reduce the risk of pouch damage, although vaginal delivery is often possible in these cases as well 

The method of delivery has shown not to affect the mother’s IBD. In some cases, women with a history of J pouch surgery will have increased nighttime bowel movements and incontinence but these symptoms were unchanged with either delivery methods. The symptoms also resolve themselves after some time. 

There is also an increased risk of disease flare in women with UC and colonic Crohn’s disease after giving birth. You should monitor your symptoms carefully and see your IBD team 6 weeks after the birth or earlier if you have problems. If you have stopped taking IBD medications, you should start taking them again as soon as possible after giving birth 

Breastfeeding with IBD 

Key points 

  • Breastfeeding is encouraged for women with IBD. 
  • Medications that are safe during pregnancy will also be safe for your nursing baby. 
  • Breastfeeding does not increase the chances of your disease flaring. 

Can I breastfeed my baby? 

Breastfeeding is a natural and beneficial option for both mother and child. In addition to providing the infant with a perfect and digestible mix of fat, protein and vitamins, it also provides a unique benefit to children at risk of developing IBD. 

Nursing or “lactating” also provides IBD benefits to you as a mum as well. It can help protect your body against IBD relapse. Breastfeeding also hasn’t been associated with an increased risk of disease flares, as some mothers might fear. 

Many women also fear that their IBD medications will harm their nursing child since the drug can be passed from the mother to the infant through her milk. However, most IBD medications excreted in breast milk are in very low concentrations that doctors consider safe for a newborn.  

The World Health Organization and most doctors recommend exclusively breastfeeding your child for the first six months of his or her life. But as always, talk to your doctor about what is right for you and your newborn. 

Vaccinating your baby 

Key points 

  • All standard vaccinations should be given to your baby, except if you have been taking anti-TNF therapy. 
  • Rotavirus and live travel vaccines should be avoided in babies exposed to anti-TNF therapy. 

Should my baby get vaccinated? 

Vaccinations are one of the easiest and most effective ways to protect your newborn child from illness. They help promote immunity to certain fatal diseases and protect your child from infections in the future. To ensure your baby gets the best possible protection from vaccines, it’s important he or she start receiving them, typically starting at two months, during the first year of life. Before vaccinating your child, your pediatrician should know of any medications you—the mother—are taking. 

The hepatitis B, DTaP, Hib, pneumococcal and polio vaccines are inactivated vaccines. That means they are made up of cells of the illness grown and killed in a lab, which the human body (even a baby’s) can learn to identify and defend against without becoming infected. These types of vaccinations are safe to administer on schedule to babies born to mothers who are currently on any IBD medication.  

However, Rotavirus vaccines, RotaTeq (RV5) or Rotarix (RV1), are both live vaccines taken by mouth. If you’re taking biologic medications (except certolizumab pegol) such as infliximab, adalimumab, vedolizumab or ustekinumab, your baby’s pediatrician should not administer the Rotavirus vaccine to your newborn. However, if you’re only taking the other types of immunosuppressive medications, such as steroids, mercaptopurine or azathioprine, then the rotavirus vaccines can typically be started on schedule. 


Around 1 in 10 people with Crohn’s and colitis report having IBD in the family history. 

2 in 3 women who are in remission pre-pregnancy will stay in remission throughout their pregnancy. 

The fear of harming their nursing child by breastfeeding while on medication was so strong that a European study reported that at one time, 60% of women with IBD stopped their medications in the postpartum period.