Pregnancy and Autoimmune Disease: Safe Medications and Preconception Planning

When you have an autoimmune disease and are thinking about having a baby, the biggest question isn’t just can I get pregnant-it’s can I stay safe while I am. Too many women are told to stop their meds the moment they start trying, only to end up in the hospital with a flare-up months later. The truth? Uncontrolled disease is far more dangerous to your baby than most medications.

Why Stopping Meds Isn’t the Answer

It’s a common myth: if you’re pregnant, you should stop everything. But data from over 1,200 studies reviewed by the European Alliance of Associations for Rheumatology (EULAR) in 2025 shows that 87% of standard autoimmune treatments are safe to keep using through conception, pregnancy, and breastfeeding. That’s not a guess-it’s based on tracking more than 50,000 pregnancies.

Take tumor necrosis factor (TNF) inhibitors like adalimumab or infliximab. If you stop them cold when you start trying to conceive, your chance of a flare jumps to 63%. If you keep them going? Only 20% flare. And flares don’t just mean joint pain or fatigue-they mean higher risks of preeclampsia, preterm birth, low birth weight, and even miscarriage.

One woman in Perth shared her story on a patient forum: she stopped her adalimumab at 8 weeks because her OB said it was “better to be safe.” By 20 weeks, she had a severe rheumatoid arthritis flare. She needed prednisone, developed gestational diabetes, and delivered at 34 weeks. Her baby spent weeks in NICU. She wasn’t reckless. She was following outdated advice.

Medications That Are Safe (and Even Helpful)

Not all drugs are created equal. Some are safe. Some are lifesavers. Here’s what the evidence says about the most common ones:

• Hydroxychloroquine: Used for lupus and rheumatoid arthritis, this drug is one of the safest. In over 12,000 pregnancies, there was no increase in birth defects. It cuts lupus flares by 66% and lowers the risk of preterm birth by half. It’s so safe, doctors recommend continuing it throughout pregnancy-even if you’re breastfeeding.
• Azathioprine: A go-to for lupus nephritis and vasculitis. Over 5,800 pregnancies show it’s safe, with only a 2.1% risk of preterm birth-far lower than the 8.7% seen when the disease itself is active.
• Sulfasalazine: Safe for RA and inflammatory bowel disease. No birth defects linked. You can keep taking it.
• TNF inhibitors: Certolizumab pegol is the standout. It barely crosses the placenta-just 0.2% of mom’s blood level. Adalimumab and infliximab cross more, but still show over 94% safety. Many doctors now recommend switching to certolizumab in the third trimester to minimize fetal exposure.
• Corticosteroids: Low-dose prednisone (under 20mg/day) is generally safe. Higher doses increase risks like gestational diabetes and high blood pressure, so the goal is always the lowest effective dose.

Medications to Stop Before Conception

Some drugs are absolutely not safe in pregnancy. These aren’t “maybe risky”-they’re known to cause serious birth defects.

• Methotrexate: This drug is a hard no. It causes craniofacial defects, limb abnormalities, and miscarriage. You need to stop it at least 3 months before trying to conceive. Some women need longer depending on dosage and how long they’ve been on it.
• Mycophenolate mofetil: Used for lupus kidney disease, this one carries a 24.4% risk of birth defects-including missing ears, cleft palate, and eye problems. The FDA black box warning says you must stop it at least 6 weeks before conception, but many experts recommend 3 months for safety.
• JAK inhibitors: Like tofacitinib and upadacitinib. EULAR says avoid them entirely. Japan’s registry shows low risk in 47 pregnancies, but global data is too thin to call it safe. Until more evidence comes in, stop them.

Here’s the key: Don’t wait until you’re pregnant to switch. If you’re on methotrexate or mycophenolate, start planning with your rheumatologist at least 6 months before you want to conceive. Switching meds takes time. Your body needs to clear the old drug and stabilize on the new one.

What About Biosimilars and Newer Drugs?

Since Humira’s patent expired in January 2023, eight biosimilar versions (like Amjevita, Hyrimoz, Hadlima) are now on the market. Good news: they’re identical in safety and effectiveness during pregnancy. If your doctor switches you to one, you’re not losing protection.

Newer biologics like tocilizumab and vedolizumab are trickier. There are only about 200 documented pregnancies total for these drugs. That’s not enough to say they’re risky-but it’s not enough to say they’re perfectly safe either. Most rheumatologists will only use them if you’ve tried everything else and your disease is still raging. In those cases, the risk of uncontrolled illness outweighs the unknown drug risk.

Preconception Planning: The Real Game-Changer

The biggest predictor of a healthy pregnancy? Planning ahead.

A 2022 study from the Lupus Foundation found that women who saw both a rheumatologist and a maternal-fetal medicine specialist before getting pregnant had:

• 53% fewer unplanned medication stops
• 37% higher rate of full-term births
• Lower rates of NICU stays and complications

That’s not luck. That’s coordination. Your rheumatologist knows your disease. Your OB knows pregnancy. But only a team that talks to each other can bridge the gap.

Here’s what a good preconception plan looks like:

1. At least 6 months before trying: Review all meds. Switch off unsafe ones.
2. Get your disease under control. Stable for at least 3-6 months before conception.
3. Start prenatal vitamins with folic acid (at least 0.8mg/day). It reduces neural tube defects and may help lower flare risk.
4. Find a specialist who knows this space-not just any OB. Look for clinics with autoimmune pregnancy programs.
5. Keep a log: Medications, symptoms, appointments. Bring it to every visit.

What About Breastfeeding?

Yes, you can breastfeed. Most biologics don’t pass into breastmilk in any meaningful amount. Adalimumab? Only 0.005% to 0.13% of mom’s blood level shows up in milk. That’s less than a drop. Hydroxychloroquine? Safe. Azathioprine? Safe. Even certolizumab, which barely crosses the placenta, is fine for nursing.

The only exception? Methotrexate and mycophenolate. Don’t breastfeed if you’re still on those. But if you’re on safe meds? Go ahead. Breastfeeding reduces your own flare risk too.

What About Anxiety? You’re Not Alone

Over two-thirds of women with autoimmune diseases report serious anxiety about medication safety. Nearly 42% quit their meds without talking to a doctor. That’s fear talking-not science.

One Reddit user wrote: “I stayed on certolizumab. Baby was born at 39 weeks, 7 lbs 10 oz. Zero problems.” Another: “I stopped everything because I was scared. Flare at 20 weeks. Preterm. Trauma.”

There’s no shame in being scared. But you don’t have to face it alone. Talk to your rheumatologist. Find a support group. Use tools like the MotherToBaby registry-they answer questions for free and track real-world outcomes.

The Future Is Getting Better

In 2024, the NIH launched a $12.7 million research network focused on autoimmune disease in pregnancy. They’re tracking 5,000 women over five years to fill the data gaps on newer drugs. EULAR is releasing a patient decision tool in late 2024. ACOG will update its guidelines in mid-2025 to match the latest science.

And the most exciting development? A prediction tool developed by Dr. Megan Clowse’s team at Duke. It uses 12 clinical factors-like your disease history, lab results, and medication use-to calculate your personal risk of flare during pregnancy. It’s 87% accurate. That means you’re not guessing anymore. You’re planning.

Bottom Line: You Can Have a Healthy Pregnancy

You don’t have to choose between being healthy and having a baby. The science is clear: with the right planning, most women with autoimmune diseases can carry a baby safely and deliver a healthy child.

Start with your rheumatologist. Don’t wait for your OB to tell you what to do. Bring the latest EULAR guidelines (2025) with you. Ask: “Is my current medication safe? Should I switch? When?”

And remember: the goal isn’t to be medication-free. The goal is to be disease-controlled. Your baby’s health depends on your health. And you’re not alone in this fight.