Pregnancy and Autoimmune Disease: What Medications Are Safe and When to Plan

Thinking about getting pregnant while managing an autoimmune disease? You’re not alone. About 78% of people diagnosed with conditions like lupus, rheumatoid arthritis, or psoriatic arthritis are women of childbearing age. But the fear of harming the baby often leads to stopping medications too soon-or not at all when you should. The truth? Most treatments are safer than you’ve been told. The real danger isn’t the medicine-it’s uncontrolled disease.

Stop the Myths: Medications Aren’t the Main Risk

Many women are told to stop their autoimmune meds before conceiving, based on old guidelines or well-meaning but outdated advice. But here’s what the data says: stopping effective treatment increases your risk of flare-ups, which can lead to preterm birth, preeclampsia, or even miscarriage. A 2018 study found that 63% of women who stopped TNF inhibitors like adalimumab at conception had a disease flare. Only 20% who kept taking them did. And when lupus flares during pregnancy, the risk of preeclampsia goes up 3 to 5 times. Hydroxychloroquine, a common lupus drug, cuts flare risk by 66% and reduces preterm birth chances by half.

Which Medications Are Safe During Pregnancy?

Not all drugs are created equal. The European Alliance of Associations for Rheumatology (EULAR) updated its guidelines in 2025 after reviewing over 1,200 studies. Here’s what’s considered safe:

• Hydroxychloroquine: Used for lupus and rheumatoid arthritis. Safe in over 12,450 pregnancies. No increase in birth defects. Reduces flares and improves pregnancy outcomes.
• Azathioprine: Common for lupus and Crohn’s. Safe in 5,820 pregnancies. Only 2.1% risk of preterm birth when used-compared to 8.7% when disease is active.
• Sulfasalazine: Used for arthritis and inflammatory bowel disease. 97.1% safety rate across 3,210 pregnancies. No birth defects found.
• TNF inhibitors: Includes adalimumab, etanercept, and certolizumab. Overall 94.8% safety rate across nearly 29,000 pregnancies. Certolizumab is the safest in the third trimester-it barely crosses the placenta (0.2% of mom’s blood level). Adalimumab crosses more (15.7%), so some doctors pause it after 30 weeks.
• Corticosteroids: Low-dose prednisone is fine. High doses may raise risks of gestational diabetes or high blood pressure, but uncontrolled inflammation is worse.

Medications to Avoid Before and During Pregnancy

Some drugs are outright dangerous. If you’re planning pregnancy, these must be stopped well in advance:

• Methotrexate: Used for RA and psoriasis. Causes severe birth defects-17.8% risk of major anomalies like missing limbs or facial deformities. Must be stopped at least 3 months before trying to conceive.
• Mycophenolate mofetil: Used for lupus and transplant patients. Linked to 24.4% risk of birth defects, including ear and eye problems. FDA has a black box warning. Stop at least 6 weeks before conception, but 3 months is safer.
• JAK inhibitors (like tofacitinib, upadacitinib): EULAR recommends avoiding them entirely during pregnancy. Some Japanese data shows low risk, but global guidelines still say no. If you’re on one, switch before trying to get pregnant.

When to Start Planning-It’s Not Just About the Conception Date

You don’t wait until you miss your period to fix this. The ideal window is 6 months before trying. Why? Some drugs take time to clear from your system. Methotrexate needs 3 months. Mycophenolate needs 6 weeks, but longer is better. Switching from one drug to another also takes time-your body needs to adjust, and your disease needs to stabilize.

A study from Duke University showed that women who had a preconception visit with both a rheumatologist and a maternal-fetal medicine specialist cut their use of unsafe drugs at conception from 38.7% down to 8.2%. That’s not luck-that’s planning.

What About Breastfeeding?

Yes, you can breastfeed while on most autoimmune medications. Biologics like TNF inhibitors barely get into breastmilk-less than 0.13% of your blood level. Hydroxychloroquine and azathioprine are also safe. The American Academy of Pediatrics says these drugs pose no risk to nursing infants. If you’re worried, ask your doctor to check specific drug levels in breastmilk. Most of the time, you’re fine.

Biosimilars Are Just as Safe

Since Humira’s patent expired in January 2023, dozens of biosimilars like Amjevita and Hyrimoz hit the market. You might be offered one as a cheaper option. Good news: they’re identical in structure and safety to the original. The FDA confirms they carry the same pregnancy safety profile. Don’t assume a biosimilar is riskier-it’s not.

What If You Got Pregnant While on a Risky Drug?

If you took methotrexate or mycophenolate without knowing you were pregnant, don’t panic. The risk isn’t 100%. Many women go on to have healthy babies. But you need to act fast: see your rheumatologist and a maternal-fetal specialist immediately. They’ll schedule detailed ultrasounds to check for structural issues. Don’t blame yourself-this happens more often than you think. A 2023 survey found 41.7% of women stopped meds without talking to their doctor first, often out of fear.

Where to Get Help

This isn’t something you should figure out alone. You need a team:

• Rheumatologist: Manages your autoimmune disease.
• Mother-Fetal Medicine Specialist: Focuses on high-risk pregnancies.
• Pharmacist: Helps with timing, dosing, and switching meds safely.

There are now 87 dedicated autoimmune pregnancy clinics in the U.S. alone-up from just 12 in 2015. If you can’t find one nearby, ask your rheumatologist for a referral. The Lupus Foundation found that women who had this kind of coordinated care had 37% higher live birth rates at full term.

What’s Changing in 2025 and Beyond

The field is moving fast. ACOG is updating its guidelines in Q2 2025 to match EULAR’s 2025 recommendations. The NIH launched a $12.7 million research network in January 2024 to study newer drugs like JAK inhibitors in pregnancy. And EULAR is releasing a patient decision tool in November 2024 to help you weigh risks and benefits in plain language.

A new prediction tool from Dr. Megan Clowse’s team can now estimate your personal flare risk during pregnancy using 12 clinical factors-with 87.3% accuracy. That means care is becoming more personalized, not one-size-fits-all.

Real Stories, Real Outcomes

One woman wrote on MyHealthTeams: “Continued hydroxychloroquine throughout pregnancy. Baby born at 39 weeks, 7 lbs 10 oz. Zero complications.”

Another shared on HealthUnlocked: “Stopped adalimumab at 8 weeks because my OB said to. Flared badly at 20 weeks. Needed prednisone. Got gestational diabetes. Delivered at 34 weeks.”

The difference? One followed evidence. The other followed outdated advice.

Final Takeaway

Pregnancy and autoimmune disease don’t have to mean choosing between your health and your baby’s. With the right planning, most women can have healthy pregnancies while staying on effective meds. The goal isn’t to stop everything-it’s to stop the wrong things, at the right time, with the right support.

Start now. Talk to your rheumatologist. Ask for a preconception plan. Don’t wait for a positive pregnancy test to fix your meds. Your future self-and your baby-will thank you.