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Autoimmune disease may affect fertility and pregnancy by disrupting hormones, damaging ovarian tissue, and triggering inflammation that interferes with conception or implantation. Conditions like lupus, Hashimoto’s thyroiditis, and antiphospholipid syndrome raise the risk of infertility, miscarriage, and pregnancy complications. With proper testing, medication, and specialist care, many people with autoimmune disease can still conceive and carry a healthy pregnancy.
Autoimmune disease and fertility are more connected than many people realize. In autoimmune disease, the immune system mistakenly attacks healthy tissue. Research shows autoimmune disease and pregnancy loss share a documented link, especially with lupus, thyroid antibodies, and antiphospholipid syndrome. Because autoimmune disease affects an estimated 23.5 to 50 million Americans, many of them women of reproductive age, understanding this connection matters for anyone planning a pregnancy or facing unexplained infertility.
Key takeaways
- Fertility risk depends on the disease. Lupus, Hashimoto’s thyroiditis, antiphospholipid syndrome, and CVID each affect fertility and pregnancy differently.
- Active disease drives most of the risk. A stable, well-managed autoimmune condition carries a much lower risk profile than an active flare.
- Autoimmune disease can affect male fertility too. Inflammation and immune activity can lower sperm quality and cause immune-related infertility.
- Specialist care may improve outcomes. Preconception counseling and a coordinated care team may help people with autoimmune disease have healthy pregnancies.
What is autoimmune fertility? How the immune system affects conception
Autoimmune conditions can affect fertility through several different mechanisms depending on the specific disease. These may include systemic inflammation, thyroid or other hormonal dysfunction, certain autoantibodies, medication effects, and, more rarely, direct involvement of reproductive tissues. Some autoimmune conditions are also associated with an increased risk of pregnancy complications or pregnancy loss. The result can be irregular cycles, poor egg quality, implantation failure, or pregnancy loss.
An estimated 75 to 80 percent of those diagnosed with autoimmunity are women, according to the NIH Office of Autoimmune Disease Research. That overlap is one reason fertility clinics increasingly screen for autoimmune markers in people with unexplained infertility or recurrent miscarriage.
Which autoimmune diseases are linked to infertility?
Several autoimmune diseases and fertility are consistently linked, most often through inflammation, autoantibodies, or hormone disruption. The most studied conditions include lupus, Hashimoto’s thyroiditis, antiphospholipid syndrome, autoimmune hepatitis, and common variable immunodeficiency (CVID). Each affects the reproductive system through a different mechanism, so treatment looks different for each one.
- Systemic lupus erythematosus (SLE): raises the risk of flares, blood clotting, and preeclampsia during pregnancy.
- Hashimoto’s thyroiditis: thyroid antibodies are linked to a 2 to 4 fold higher risk of miscarriage and preterm birth.
- Antiphospholipid syndrome (APS): causes blood clots that can damage the placenta and lead to recurrent pregnancy loss.
- Autoimmune hepatitis: may complicate pregnancy, especially with cirrhosis, though most pregnancies still result in live births with monitoring.
- CVID: an immunodeficiency rather than a classic autoimmune disease, but one that often overlaps with autoimmune conditions and needs immunoglobulin support during pregnancy.
Here is how these conditions compare, alongside PMOS (Polycystic Ovary Syndrome), which is commonly asked about but is not classified as autoimmune:
| Condition | Autoimmune? | How it can affect fertility or pregnancy | Key management step |
|---|---|---|---|
| Systemic lupus erythematosus (SLE) | Yes | Flares, blood clotting risk, and preeclampsia during pregnancy | Preconception counseling; low-dose aspirin |
| Hashimoto’s thyroiditis | Yes | Thyroid antibodies can sometimes be linked to higher miscarriage and preterm birth risk | TSH monitoring; levothyroxine |
| Antiphospholipid syndrome (APS) | Yes | Placental blood clots; recurrent pregnancy loss | Low-dose aspirin plus heparin |
| CVID | Immunodeficiency, overlaps with autoimmune disease | Low antibody levels raise infection and miscarriage risk | Immunoglobulin replacement therapy |
| PMOS | No, hormonal and metabolic | Anovulation and irregular cycles, not an immune attack | Ovulation induction; insulin management |
How does autoimmune disease affect egg quality and ovarian reserve?
Autoimmune disease can lower egg quality and ovarian reserve mainly through chronic inflammation and thyroid dysfunction. In Hashimoto’s thyroiditis, elevated TSH has been linked to lower blastocyst formation, and some studies show slightly lower anti-Müllerian hormone (AMH) levels and immature egg counts in affected women.
In the Journal of Clinical Medicine, Emilia Popa and colleagues studied 86 women undergoing fertility evaluation in 2025 and found that those with thyroid antibodies had significantly lower blastocyst formation (vital for implantation), tied to elevated TSH, even though egg counts did not differ significantly between the groups.
Another concern is oophoritis. Autoimmune oophoritis occurs when antibodies attack ovarian tissue, damaging egg-producing follicles and lowering ovarian reserve. It is a rare but recognized cause of primary ovarian insufficiency, sometimes appearing alongside autoimmune Addison’s disease or thyroid disease.
Because it is rare and hard to test for directly, autoimmune oophoritis is usually diagnosed only after ruling out other causes of early ovarian decline.
What’s the link between autoimmune disease and pregnancy loss?
Autoimmune disease and fertility affect pregnancy loss mainly through two mechanisms: autoantibodies that damage the placenta, and disease flares that stress the body during pregnancy. Antiphospholipid syndrome causes clotting that can starve the placenta of blood flow, while active lupus increases the risk of preeclampsia and fetal growth restriction.
Guidance from the Society for Maternal-Fetal Medicine notes that pregnancies affected by active lupus nephritis carry a substantially higher risk of preeclampsia, fetal growth restriction, and preterm delivery than pregnancies in patients with stable disease.
For a woman who has already had a pregnancy affected by congenital heart block, the risk of recurrence in a later pregnancy is roughly 17 to 18 percent, and higher if more than one prior pregnancy was affected, which is why specialists recommend closer fetal heart monitoring in those pregnancies. For an antibody-positive woman who has not had an affected pregnancy, the baseline risk is much lower, around 1 to 2 percent.
Does autoimmune disease affect fertility in men?
Yes. Autoimmune disease can affect male fertility through inflammation that lowers sperm count and motility, autoimmune attacks on testicular tissue, or antisperm antibodies that interfere with fertilization. Conditions like autoimmune thyroiditis, type 1 diabetes, and rheumatoid arthritis have all been associated with reduced semen quality.
Men with autoimmune disease who are struggling to conceive should ask about a semen analysis and antisperm antibody testing, since immune-related male infertility is often overlooked in fertility workups that focus mainly on the female partner.
How can you get pregnant with an autoimmune disease? Treatment options explained
Many people with autoimmune disease can conceive with the right preparation:
- Get preconception testing, consider requesting in depth testing that extends to testing for antibodies, thyroid function, and disease activity markers.
- Work with your specialist to stabilize your condition for several months before trying to conceive.
- Review every medication with your doctor, since some immunosuppressants aren’t safe in pregnancy.
- Ask about low-dose aspirin or another preventive treatment if you have antiphospholipid syndrome.
- Build a care team that includes your rheumatologist, endocrinologist, or immunologist alongside your OB-GYN.
- Track your cycle using the Premom app to help understand your body and your fertility.
Medications and fertility treatment considerations
Some autoimmune medications, including methotrexate and mycophenolate mofetil, should be stopped well before conception because they may cause birth defects, while others, such as hydroxychloroquine and low-dose steroids, are generally considered safe to continue. Never stop or adjust a medication without your specialist’s guidance.
Such a specialist might be a reproductive immunologist who specializes in immune-related infertility and recurrent pregnancy loss, testing for antiphospholipid antibodies, thyroid antibodies, and other immune markers that a standard fertility workup may miss. They can also help time immune-modulating treatment around IVF or a natural conception attempt.
How do you manage autoimmune disease during pregnancy?
Managing autoimmune disease during pregnancy means treating it as a high-risk pregnancy: more frequent monitoring, careful medication management, and close coordination between your OB-GYN and your specialist. Bloodwork tracks disease activity, ultrasounds monitor fetal growth, and some conditions require fetal heart monitoring for neonatal lupus risk. There are also sometimes diet, lifestyle and medications that are also implemented.
Because immunosuppressive treatment can raise infection risk, your care team will also watch for chorioamnionitis, an infection of the membranes around the baby that can trigger preterm labor. If a baby is born with jaundice or anemia linked to maternal antibodies, sometimes called hemolytic disease of the newborn, many cases resolve with monitoring and phototherapy as the antibodies clear from the baby’s system.
The information provided in this article is for educational and informational purposes only and is not intended as medical advice. Always consult with a qualified healthcare professional or OB-GYN regarding any questions you may have about your menstrual cycle, reproductive health, or medical conditions.
Key terms explained
- Autoimmune disease: a condition in which the immune system mistakenly attacks the body’s own healthy tissue, causing inflammation and, in some cases, organ damage.
- Antiphospholipid syndrome (APS): an autoimmune clotting disorder in which antibodies raise the risk of blood clots, placental damage, and recurrent miscarriage.
- CVID (common variable immunodeficiency): a primary immunodeficiency marked by low antibody levels, raising infection risk and sometimes overlapping with autoimmune disease.
- Hypogammaglobulinemia: abnormally low levels of antibodies in the blood, which can be a standalone condition or a feature of disorders like CVID.
- Chorioamnionitis: an infection or inflammation of the membranes surrounding a fetus, linked to preterm labor and more common in people on immune-suppressing medication.
- Hemolytic disease of the newborn: a condition where maternal antibodies cross the placenta and destroy the baby’s red blood cells, causing jaundice or anemia.
- Immunocompromised: having a weakened immune system, whether from disease, medication, or another cause, that increases vulnerability to infection.
