Does Autoimmune Disease Put Your Fertility And Pregnancy At Risk?

There are more than 100 autoimmune diseases that can affect almost every organ and tissue in the human body. The nerves, muscles, endocrine glands, gastrointestinal tract and connective tissue can be damaged or destroyed as a result of the autoimmune attack.

About 75% of autoimmune conditions affect women most frequently during the childbearing years and can interfere with their fertility and ability to have children. Research studies show that fertility is reduced even before clinical diagnosis of many autoimmune diseases is made.

Subclinical autoimmunity can affect reproductive function, fertility and lead to pregnancy complications such as recurrent miscarriage, increase in incidence of other health conditions in mothers during and after pregnancy (gestational diabetes, preeclampsia, postpartum depression, postpartum thyroiditis etc.), increased fetal loss and death.

While women over 50 are the biggest group at risk to develop autoimmune thyroid disease such as Hashimoto’s and Grave’s, more and more younger women who are in their 20s and 30s and ready to have children are getting diagnosed with these conditions.

Hashimoto’s disease can take up to 10 years to progress from subclinical state to a full blown hypothyroidism and during this time a woman may not show any symptoms or not be aware that she has the disease.

To ensure successful pregnancy, women with clinical and subclinical autoimmune diseases need medical care before, during and after pregnancy.


It should be one of the priorities to identify if autoimmunity is present and is a factor that contributes to infertility in women who have difficulties getting pregnant. Studies show that women with Hashimoto’s and other autoimmune diseases are more likely to have fertility problems compared to healthy women who are trying to conceive.

There are 5 common ways how autoimmunity can affect fertility:

1. Some women who have problems with their fertility actually have undiagnosed underlying autoimmune or thyroid problems. The presence of high thyroid antibodies can directly result in infertility and pregnancy loss even in women who have normal thyroid function and do not show any hypothyroid symptoms. Studies show that high TPO thyroid antibodies are commonly found in infertile women.

Besides Hashimoto’s disease, other autoimmune conditions such as rheumatoid arthritis, myasthenia gravis, antiphospholipid syndrome, Grave’s disease, lupus (SLE), type 1 diabetes mellitus are also linked to infertility and pregnancy complications even before the disease onset.

High antiphospholipid antibodies (APA) is one of  the indicators that are helpful for identifying women at risk for fetal death, recurrent miscarriage, late pregnancy loss and women who experience infertility due to endometriosis, inability to get pregnant after in vitro fertilization or embryo transfer procedures and have unexplained infertility.

2. Many autoimmune conditions such as autoimmune hepatitis, autoimmune oophoritis (premature ovarian failure) can result in menstrual irregularities or absence of periods making it hard or impossible for some women to become pregnant.

If Hashimoto’s disease has progressed to hypothyroidism and there is a deficiency of thyroid hormones the chances for infertility increase. Both hyperthyroidism and hypothyroidism can cause menstrual irregularities and interfere with ovulation in women and reduce sperm count in men. It is important to correct thyroid dysfunction and lower thyroid antibodies before conception and pregnancy.

3. Fertility can be affected during the autoimmune flare ups which are common in women with lupus and multiple sclerosis.

4. Polycystic ovary syndrome (PCOS) is one of the leading causes of infertility. According to statistics, as many as 4 out of 10 women with PCOS have some sort of autoimmune involvement and up to 27% of PCOS women have elevated thyroid antibodies.

5. Endometriosis is another common cause of infertility that is associated with many autoimmune conditions and has been thought to be an autoimmune disease itself. This type of infertility is more common in organ specific autoimmune diseases such as Hashimoto’s compared to systemic conditions such as lupus and rheumatoid arthritis.


The main goal of supportive care is to ensure healthy pregnancy and prevent pregnancy loss and complications.

Some autoimmune conditions such as multiple sclerosis, autoimmune hepatitis, rheumatoid arthritis, Hashimoto’s and Grave’s disease can go into remission during the pregnancy. This happens due to the immune-suppressive effect of pregnancy and raising female hormones of estrogen and progesterone.

A healthy immune system is dynamic and is able to switch back and forth as required depending on the type of threat to the women’s body. During pregnancy the balance of TH1 and TH2 naturally shifts to prevalence of TH2 initially to ensure that mother’s immune system does not reject the fetus and to support successful pregnancy.  A progressive shift towards TH1 predominance occurs in the last months of pregnancy and after delivery. Dysregulation of TH1 and TH2 cells is associated with autoimmune flair ups in the mother and adverse pregnancy outcome such as fetus implantation failure and recurrent pregnancy loss.

Shifts of the immune system from TH1 to TH2 can be one of the explanations why multiple sclerosis, rheumatoid arthritis and Hashimoto’s that are mostly TH1 dominant can go into remission but women with lupus who are TH2 dominant experience more flair ups during the pregnancy.

The effect of pregnancy on lupus is controversial. Studies show that women with lupus have significantly more autoimmune flair ups during the pregnancy compared to those with SLE who are not pregnant.

Remission of hyperthyroidism is observed in about 50% of patients with Grave’s disease. Partial recovery of thyroid function and shrinking of the goiter often occur during the pregnancy in women who have Hashimoto’s with goiter and hypothyroidism.

Another contributing factor is hormone progesterone that has been shown to have a protective effect on the fetus, support thyroid function and contribute to remission of some autoimmune conditions. During pregnancy progesterone levels slowly rise until the term and become several hundred times higher compared to the levels before conception. Adequate progesterone levels contribute to general well-being and many women report that they feel good while pregnant and their autoimmune disease goes into remission.

On the opposite, if the body is not able to keep up with increasing requirements for progesterone a woman cannot sustain the pregnancy and a miscarriage can occur at any stage of the pregnancy.

Thyroid hormone and iodine requirements increase during the first trimester of pregnancy and are necessary for normal fetus and child development and growth. The failure of the mother’s thyroid gland to produce adequate levels of thyroid hormones can result in a higher risk of cognitive impairment, lower IQ and problem behavior in a child, in particular, attention deficit and hyperactivity disorder.

Some studies suggest a possible association between autism and autoimmune disease. A frequency of autoimmune disorders in the first- and second-generation relatives of children with autism was found to be significantly higher compared to both families with autoimmune conditions and those who are healthy. An increased occurrence of autoimmune diseases such as hypothyroidism/Hashimoto’s disease, rheumatoid arthritis and rheumatic fever was established in parents and especially mothers of children with autism.

After delivery

The main goal of medical care after delivery is to prevent possible complications in the mother and baby and monitor for the autoimmune flare ups in the mother. Autoimmune conditions that go into remission during the pregnancy very often are followed by a flare up after delivery. Relapses are often observed in women who were diagnosed with multiple sclerosis, Hashimoto’s and Grave’s diseases.

Up to 70% of women with Grave’s disease experience return of hyperthyroid symptoms immediately after delivery. Those with Hashimoto’s disease also often have a return of hypothyroidism, however postpartum thyroiditis is even a more frequent condition that is related to thyroid dysfunction and occurs during the first 3 to 6 months after pregnancy.

Women who have genetic predisposition to thyroid autoimmunity, diagnosed with type 1 diabetes mellitus and have elevated thyroid antibodies before and/or during pregnancy are more likely to experience postpartum thyroiditis. In this condition women go through a period of thyrotoxicosis with hyperthyroid symptoms that can be followed by hypothyroid symptoms later on.

A complete recovery of thyroid function occurs in 90% of women within 18 to 24 months after the onset of postpartum thyroiditis. However, up to 70% of women with history of postpartum thyroiditis will develop it in their future pregnancies and remain at high risk to progress to Hashimoto’s disease during their life time.

After giving birth progesterone levels drop dramatically and it predisposes many women to postpartum depression or so-called “maternity blues”. As many as 30% of women report to have acute sadness, insomnia, difficulty to concentrate, irritability, headaches and bouts of tears.

After delivery, progesterone levels decrease rapidly within the first 10 days and most women experience the strongest symptoms of postpartum depression between day 4 and 5. If progesterone levels remain chronically low a longer-lasting episode of major depression can develop.

How to support healthy pregnancy?

While pregnancy in women with most autoimmune diseases is still classified as high risk, it is absolutely possible to have healthy pregnancy and full-term children.

Research studies show that with adequate treatment of autoimmune disease prior and during the pregnancy, prognosis for mother and child has significantly improved compared to two decades ago. If a pregnancy is planned during the periods when an autoimmune disease is inactive or stable the prognosis is good and there are no increased risks of complications.

If a woman has unexplained infertility and/or recurrent miscarriages, tests for autoimmune disease and thyroid function can give some insights.Most women who have clinical or subclinical autoimmune disease have elevated or high antibodies that can be used as one of diagnostic criteria. Comprehensive screening for systemic autoimmunity can be useful in order to determine what types of antibodies are present and what organs and tissues are affected.

Standard care for lupus, APS, multiple sclerosis and other inflammatory autoimmune diseases before and during the pregnancy is immunosuppression with cortisone, blood thinners, anticoagulants or intravenous immunoglobulin (IVIG) to temporarily decrease immunological reactions. Many brands of corticosteroids are not recommended for use during pregnancy.

Thyroid hormones can and should be taken during pregnancy if any indications are found.

However, conventional medicine offers limited treatment options or no treatment at all for subclinical autoimmune conditions while high levels of antibodies pose a high risk for infertility and healthy pregnancy.

One of the new proposed strategies for reducing antibodies and to balance the immune system is an anti-autoimmune diet for fertility and pregnancy and time of breastfeeding. Before a woman becomes pregnant, it is important for her to have good nutrition and a healthy lifestyle. Mother’s diet has a long-lasting effect on the health of the baby and can help to avoid or reduce the risk of many diseases in the child.

Diet for women with subclinical and clinical autoimmune conditions should reduce the risk of autoimmune reactions before, during and after pregnancy by identifying and removing all dietary triggers and including foods that boost fertility and support thyroid function.

However, most practitioners stop right there and do not take into consideration HOW the environmental and dietary factors actually trigger the autoimmune disease. There is a new theory how autoimmunity can be activated and it involves not only genetic and environmental triggers but also a new component that connects it all together.

I have a full article on how this new discovery can help to prevent and heal autoimmune disease.



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The implications of autoimmunity and pregnancy.  J Autoimmun. 2010 May;34(3):J287-99. Epub  2009 Dec 23. 

Maternity blues and major endocrine changes: Cardiff puerperal mood and hormone study II. BMJ 1994;308:949-953 (9 April).

 Increased prevalence of familial autoimmunity in probands with pervasive developmental disorders.  Pediatrics. 2003 Nov;112(5):e420.

Differential actions of glycodelin-A on Th-1 and Th-2 cells: a paracrine mechanism that could produce the Th-2 dominant environment during pregnancy. Hum Reprod. 2011 Mar;26(3):517-26. Epub  2011 Jan 11.



About Marina Gutner, PhD

Marina Gutner, PhD, researcher, medical writer, thyroid blogger, founder and Admin of Outsmart Disease who writes about life-changing treatments for hypothyroidism, Hashimoto's thyroiditis and autoimmune disease and how to balance hormones in women