Pregnancy and Autoimmune Disease: Medication Safety and Planning

When you have an autoimmune disease and are thinking about getting pregnant, the biggest question isn’t just can I get pregnant? It’s can I stay healthy-and can my baby?

For years, the advice was simple: stop all your meds. But that advice is outdated. In fact, stopping your medication without a plan can be riskier than keeping it. The latest research shows that uncontrolled disease poses a far greater threat to both mother and baby than most of the drugs used to manage it.

Why This Isn’t Just About Stopping Pills

Autoimmune diseases like lupus, rheumatoid arthritis, and psoriatic arthritis don’t just go away when you get pregnant. In fact, they often flare. And when they do, the risks go up: preterm birth, preeclampsia, low birth weight, even stillbirth. A study from Duke University found that women with active lupus during pregnancy were three to five times more likely to develop preeclampsia than those whose disease was under control. The same study showed that hydroxychloroquine, a common lupus drug, cuts flare risk by 66% and lowers the chance of preterm birth by half.

So here’s the truth: it’s not about avoiding medication. It’s about choosing the right ones-at the right time.

What Medications Are Safe? The Data Doesn’t Lie

Let’s cut through the noise. There are now clear, evidence-based guidelines from the European Alliance of Associations for Rheumatology (EULAR), updated in February 2025, that cover 47 different drugs. Here’s what the numbers say:

• Hydroxychloroquine (used for lupus and RA): 98.7% safety rate across over 12,000 pregnancies. No increase in birth defects. It’s so safe, it’s recommended to continue-even through breastfeeding.
• Azathioprine: 95.3% safe. Only 2.1% of babies born to moms on this drug were preterm, compared to 8.7% if the disease itself was active.
• Sulfasalazine: 97.1% safe. No signs of harm to the baby.
• TNF inhibitors (adalimumab, infliximab, etanercept, certolizumab): 94.8% safe across nearly 30,000 pregnancies. But not all are equal. Certolizumab pegol transfers almost nothing to the baby-just 0.2% of the mom’s blood level. Adalimumab? 15.7%. Infliximab? 23.4%. That’s why certolizumab is often preferred for third-trimester use.

And here’s the kicker: if you stop your TNF inhibitor before pregnancy, you have a 63% chance of a flare. If you keep it? Only 20%.

The Drugs You Must Stop-Before You Get Pregnant

Some medications are dangerous during pregnancy. Not because they’re “bad,” but because they’re too powerful. These are not up for debate:

• Methotrexate: This one is a hard stop. It’s linked to 17.8% risk of major birth defects-cleft palate, missing limbs, skull deformities. You need to stop it at least three months before trying to conceive.
• Mycophenolate: This one is even scarier. It causes serious birth defects in 24.4% of cases-missing ears, eye problems, heart defects. The FDA added a black box warning in March 2023. You need to switch at least six weeks before conception, but many doctors recommend three months.
• JAK inhibitors (tofacitinib, upadacitinib): EULAR says avoid entirely. Japan’s guidelines say it might be okay in the first trimester, but U.S. and European experts say the risk isn’t worth it. No one’s saying “yes” here yet.

Here’s what patients tell us: women who stopped methotrexate on their own, without doctor guidance, often had unplanned pregnancies and ended up with scary outcomes. One woman on Reddit wrote: “Stopped adalimumab at 8 weeks because my OB said ‘better safe than sorry.’ Flared badly by 20 weeks. Ended up on prednisone. Got gestational diabetes. Baby born at 34 weeks.”

Preconception Planning: The 6-Month Rule

You wouldn’t start a marathon without training. Why start a pregnancy without planning?

The best outcomes come from a team: a rheumatologist, a maternal-fetal medicine specialist, and a pharmacist. They meet at least six months before you try to conceive. Here’s what they do:

1. Review every medication you’re on.
2. Switch unsafe drugs to safer ones-like switching from methotrexate to azathioprine.
3. Check your disease activity. Are you in remission? If not, get it there before pregnancy.
4. Update your vaccines (flu, whooping cough, COVID-19). Live vaccines? Avoid during pregnancy.
5. Start prenatal vitamins with folic acid (at least 0.8 mg daily). This reduces birth defect risk even further.

At Duke’s pregnancy clinic, this kind of planning dropped unsafe medication use at conception from 38.7% down to 8.2%. That’s not luck. That’s planning.

What About Breastfeeding?

Yes, you can breastfeed. And yes, most of your medications are safe.

Biologics like adalimumab, certolizumab, and infliximab barely make it into breast milk. Studies show levels are 0.005% to 0.13% of the mom’s blood concentration. That’s like a drop in an ocean. The American Academy of Pediatrics says these drugs are compatible with breastfeeding.

Hydroxychloroquine? Safe. Azathioprine? Safe. Even corticosteroids? Safe-unless you’re taking more than 20 mg daily, and even then, you can usually keep going with monitoring.

One mom wrote on MyHealthTeams: “Continued hydroxychloroquine throughout pregnancy-baby born at 39 weeks, 7 lbs 10 oz, zero complications. Breastfed for 14 months.”

What About Biosimilars?

Since Humira’s patent expired in January 2023, eight biosimilars have hit the market: Amjevita, Hyrimoz, Hadlima, and others. You might be prescribed one. Should you worry?

No. The FDA says they’re identical in safety and effectiveness to the original. If adalimumab is safe in pregnancy, so is Amjevita. Same drug. Same packaging. Same science.

What’s Still Unknown?

There’s a gap. For newer drugs like vedolizumab or tocilizumab, we only have data from a few hundred pregnancies. That’s not enough. So doctors can’t say “definitely safe”-only “likely safe.”

That’s why the NIH launched a $12.7 million research network in January 2024. They’re tracking 5,000 pregnant women on newer biologics over five years. Results will come in stages, but we’ll know more by 2027.

What Should You Do Right Now?

If you’re thinking about pregnancy:

• Don’t stop your meds on your own. Flares are dangerous.
• Don’t wait until you’re pregnant to ask about safety.
• Find a rheumatologist who works with maternal-fetal specialists. Ask if they’re part of a pregnancy autoimmune clinic.
• Bring a list of every medication, supplement, and over-the-counter pill you take.
• Ask: “What’s my plan? What do I switch? When? How long before I try?”

And if you’re already pregnant and unsure about your meds? Don’t panic. Call your rheumatologist today. You’re not alone. More than 78% of autoimmune diagnoses happen in women of childbearing age. You’re part of a growing community-and we now have the science to support you.