Trying to conceive with an autoimmune condition can feel complicated.

You may be balancing symptom control, inflammation, medication safety, fertility treatment, and pregnancy planning all at once.

One of the biggest questions is:

Can I keep taking my medication while trying to get pregnant?

The answer depends on the medication, your diagnosis, your disease activity, your fertility timeline, and your care team’s recommendations.

Some autoimmune medications are generally considered compatible with conception and pregnancy.

Others may need to be stopped months before trying to conceive.

And some require a careful switch to a safer alternative before pregnancy.

The most important thing to remember is this:

Do not stop or change medication on your own.

Uncontrolled autoimmune disease can also increase pregnancy risks. For many people, the safest plan is not “no medication.” It is the right medication at the right time with the right monitoring.

This guide walks through eight key medication categories to review with your provider before conception or pregnancy.

This article is for informational purposes only and is not intended to provide medical advice. Always consult your healthcare provider, rheumatologist, OB-GYN, maternal-fetal medicine specialist, fertility specialist, psychiatrist, or pharmacist before stopping, starting, or changing any medication before conception, during fertility treatment, during pregnancy, or while breastfeeding.

Autoimmune disease and pregnancy require careful planning.

The goal is usually to enter pregnancy with your condition as stable and well-controlled as possible.

This matters because active autoimmune disease may increase the risk of complications such as:

At the same time, certain medications can affect embryo development or pregnancy safety.

That is why preconception planning is so important.

Ideally, your medication plan should be reviewed before you start trying to conceive.

This gives your care team time to:

Methotrexate is commonly used for autoimmune and inflammatory conditions such as rheumatoid arthritis and psoriasis. It is also used in other medical settings, including certain cancer treatments and ectopic pregnancy management.

Methotrexate is contraindicated in pregnancy.

It is considered unsafe because it can interfere with folate metabolism and fetal development.

It has been linked with serious pregnancy risks and birth defects.

If you take methotrexate, talk with your provider well before trying to conceive.

Your care team may discuss:

Some medications used for severe autoimmune disease, organ involvement, or transplant-related conditions require extra caution before pregnancy.

This group includes:

These medications are generally contraindicated during conception and pregnancy because of significant fetal risk.

They are not usually recommended when actively trying to conceive.

These medications may require a carefully timed transition.

For example, leflunomide may require a specific washout process because it can stay in the body for a long time.

Cyclophosphamide may also affect fertility directly and may prompt fertility preservation discussions before treatment in some cases.

Before trying to conceive, ask your care team about:

Hydroxychloroquine, often known by the brand name Plaquenil, is commonly used for conditions such as lupus, rheumatoid arthritis, and certain autoimmune skin or joint conditions.

Hydroxychloroquine is generally considered compatible with pregnancy for many patients.

It is commonly continued during pregnancy, especially in lupus, because it may help reduce disease flares and support better outcomes.

For some autoimmune conditions, stopping hydroxychloroquine may increase flare risk.

And flare prevention can be very important during pregnancy.

Your provider will weigh your diagnosis, dose, disease activity, and pregnancy plan.

Ask your doctor about:

Some autoimmune medications are commonly used during conception and pregnancy when needed for disease control.

This category includes:

These medications are often considered compatible with pregnancy when used appropriately and monitored.

However, dose, diagnosis, and side effects matter.

Sulfasalazine may be used in rheumatoid arthritis, inflammatory bowel disease, and other inflammatory conditions.

Your provider may recommend folic acid supplementation when taking sulfasalazine.

Azathioprine is used for conditions such as lupus, inflammatory bowel disease, vasculitis, and transplant-related immune suppression.

It is often used in pregnancy when the benefits outweigh the risks.

Your provider may consider enzyme testing, dosing, and monitoring.

Steroids can be useful for flares and inflammation control.

However, long-term or higher-dose steroid use may increase risks such as:

The goal is usually the lowest effective dose when steroids are needed.

TNF-alpha inhibitors are biologic medications used for autoimmune and inflammatory diseases.

Examples may include:

These may be used for conditions such as rheumatoid arthritis, Crohn’s disease, ulcerative colitis, psoriasis, psoriatic arthritis, and ankylosing spondylitis.

TNF-alpha inhibitors are often considered compatible with pregnancy when disease activity requires treatment.

However, the specific medication matters because different biologics cross the placenta differently, especially later in pregnancy.

Your provider may discuss whether to continue throughout pregnancy or adjust timing near delivery.

This can affect:

Some biologics may influence when a baby can receive certain live vaccines.

This should be discussed with your OB and pediatrician.

Some autoimmune medications have less pregnancy safety data.

These may include certain non-TNF biologics and small molecule disease-modifying drugs.

Examples may include:

These medications are often handled on a case-by-case basis.

Some may be avoided before conception unless the benefits clearly outweigh the risks.

Others may require a planned delay before trying to conceive.

Rituximab may affect B cells and immune function.

If used close to pregnancy, your provider may discuss possible effects on newborn immune function and monitoring.

Ask your care team about:

NSAIDs are nonsteroidal anti-inflammatory drugs used for pain and inflammation.

Common examples include:

NSAID safety depends on timing, dose, and reason for use.

Short-term use before conception or early in pregnancy may be allowed in some cases, but you should ask your provider.

NSAIDs are generally avoided later in pregnancy because of risks such as low amniotic fluid and effects on the baby’s heart circulation.

Low-dose aspirin is different from typical NSAID use and may be specifically recommended for some pregnancy-related conditions, but only under medical guidance.

High-dose or frequent NSAID use around ovulation may affect follicle rupture in some people.

If you are actively trying to conceive, ask whether NSAIDs are appropriate during your fertile window.

Lithium is not an autoimmune medication, but it may come up in pregnancy planning for people with bipolar disorder or overlapping psychiatric and autoimmune care.

Mental health stability is an important part of pregnancy safety.

Lithium may carry pregnancy risks, including a small increased risk of certain heart defects.

However, stopping lithium abruptly can also be risky for some people due to relapse risk.

This decision should always be made with a psychiatrist and OB or maternal-fetal medicine specialist.

If lithium is part of your treatment plan, your provider may discuss:

Uncontrolled autoimmune disease can be risky during conception and pregnancy.

A medication that keeps inflammation controlled may sometimes be safer than stopping treatment and triggering a flare.

Some medications require weeks or months to clear before pregnancy.

Do not wait until a positive pregnancy test to ask about safety.

If your current medication is not pregnancy-compatible, your provider may be able to switch you to a safer option before you start trying.

Your care team may include:

Certain medications, especially biologics, may affect newborn monitoring or vaccine timing.

Ask about this before delivery so your pediatrician has the full picture.

Before trying to conceive, create a medication plan with your providers.

Include:

For every medication, ask:

Your timeline may include:

Make sure your fertility doctor and autoimmune specialist are on the same page.

This is especially important if you are doing IVF, using immune-modulating medications, or have a history of flares, pregnancy loss, or organ involvement.

Pregnancy is not the only period to plan for.

Postpartum flares can happen in some autoimmune conditions.

Ask your care team how medication, breastfeeding, sleep disruption, and disease monitoring will be handled after delivery.

Bring these questions to your next appointment:

Managing autoimmune disease while trying to conceive can feel overwhelming, but you do not have to figure it out alone.

The safest path is usually not guessing, stopping everything, or waiting until pregnancy happens.

The safest path is planning early.

Review your medications.

Ask about washout periods.

Discuss safer alternatives.

Coordinate your specialists.

And make sure your condition is as controlled as possible before pregnancy.

For many people with autoimmune disease, healthy conception and pregnancy are possible with the right plan.

Your medication plan should protect both your fertility goals and your long-term health.

You deserve a care team that helps you make informed, confident decisions every step of the way.