woman sitting on black chair in front of glass-panel window with white curtains

 Autoimmunity (AI) is best described as a confused immune system that sees you as a dangerous invader and mounts a detrimental attack. Over 4% of people globally are affected by one or sometimes multiple of the approximately 80 autoimmune diseases, with the most common diagnoses being thyroid-based (Hashimoto’s and Graves diseases), rheumatoid arthritis, vitiligo, type 1 diabetes, pernicious anemia, multiple sclerosis, and systemic lupus erythematosus or lupus (2, 3). But how are infertility, miscarriage, and autoimmune disease connected?

Uncontrolled autoimmune issues, including those not yet diagnosed, can lead to problems during the reproductive years. The cross-talk between inflammation and hormonal imbalances affects fertility and increases the risk of miscarriage. Some autoimmune issues may even increase the risk of complications during pregnancy. 

Miscarriage and autoimmune disease are more closely linked for specific diagnoses—celiac disease, thyroid disorders, systemic lupus erythematosus, and antiphospholipid antibody syndrome may be more problematic than other diseases, for instance.

Interestingly, there is also a reverse association—pregnancy can affect autoimmunity. Hormonal changes that occur during pregnancy may trigger autoimmune flares or remission, depending on the situation. 

In this blog, we’ll practically cover what to consider before conception if autoimmune disease is part of your medical history, the links between infertility, miscarriage, and autoimmune disease, and finally, pregnancy’s effect on autoimmunity. 

Infertility, miscarriage, and autoimmune disease: What to consider before conception


As part of your preconception planning, consider two important details:

  • If you’re struggling to conceive and/or have a pattern of pregnancy loss, get the medical care you need to identify whether or not you have an autoimmune issue. Unfortunately, this is sometimes a difficult diagnosis, as most autoimmune diseases differ widely by symptom and don’t have set diagnostic markers. 

However, if you have a strong family history of autoimmunity, symptoms that seem indicative of immune imbalance, or you simply feel deep down that something is off, seek care from a licensed clinician who will listen to your concerns and provide comprehensive support. 

  • If you have an autoimmune condition, ensure it’s managed throughout the preconception period and the months before you plan to conceive. Additionally, discuss your medications and supplements with your medical team so you know they are safe to take during preconception and pregnancy. 

For example, methotrexate is often used to treat autoimmune conditions such as inflammatory bowel diseases, rheumatoid arthritis, lupus, psoriasis, and psoriatic arthritis, as well as to treat ectopic pregnancy. 

But it can lead to decreased levels of maternal folate and an increased risk of congenital disabilities when used by females during preconception and pregnancy. Some sources, however, have concluded that the risk is minimal as long as the pregnant person discontinues the medication as soon as possible (4, 5). 

Conversely, while some key studies haven’t revealed an increased risk of congenital disabilities in the offspring of males exposed to methotrexate in the preconception window (6, 7), the FDA recommends that couples wait three months after paternal methotrexate use to conceive (8).

“Pregnancy should be avoided if either partner is receiving methotrexate; during and for a minimum of three months after therapy for male patients, and during and for at least one ovulatory cycle after therapy for female patients” (8). 

Infertility and autoimmune disease

Multiple direct, indirect, and overlapping connections exist between infertility and autoimmunity. This complicated web linking one to the other can be frustrating for people trying to conceive. 

This section will cover some specifics that may be useful if you are experiencing infertility and an autoimmune diagnosis. 

How are they connected?

The most studied connections between infertility and autoimmune disease include:

  • any immune process that affects hormonal balance or the reproductive organs, usually the ovaries or testes
  • the presence of some autoantibodies, such as antiphospholipid antibodies or anti-nuclear antibodies, though other antibodies may be problematic
  • autoimmune-associated diagnoses such as endometriosis or PCOS
  • levels of systemic inflammation
  • the use of certain medications, such as cyclophosphamide or even corticosteroids (9, 10, 11)

Autoimmune diseases, which by definition are highly inflammatory processes, have been linked to DOR (diminished ovarian reserve) (Sharif et al., 2019). An estimated 10–40% of women with ovarian insufficiency are also diagnosed with an autoimmune disease (Sharif et al., 2019) (10).

The challenge comes in applying these to you and your specific situation, especially if you do not have an AI diagnosis but suspect one. 

So, what do you do? 

The most critical place to start is with a trusted, licensed clinician who can help guide you through your symptoms and concerns. Combined with this, a knowledgeable nutritionist or health coach can be a fantastic support. 

However, specific monitoring and tests must occur for most cases of infertility, especially if the issue is connected to autoimmunity. And a licensed clinician is the person to guide you in this process. 

Beyond investigating this link with your care team, there are steps you can take to address hormonal imbalance and inflammation. 

Practical steps 


First, do your best to eat as many whole foods as possible. This can be tough for some people who are used to the taste and convenience of processed foods. But it can make an incredible difference in how you feel and your ability to conceive. 

Most people feel wonderful when incorporating colorful plant foods into their diets. So, try to add one new colorful vegetable or fruit per week into your family’s meal rotation.

And make sure that proteins are on the menu, too, ideally from pastured and organic animal sources. Beef, bison, venison, lamb, goat, turkey, chicken, and fish are bursting with fertility and immune-supportive nutrients. 

On the other side of the dietary coin, it can be helpful to go through an elimination/reintroduction diet. This is a protocol that helps you determine reactive foods that can increase inflammation. 

Be aware that different people react to different foods, and the list is highly unique to each individual. 

While some people do well with grains, for instance, others do not. The same goes for most foods, so please take the “reintroduction” part of the elimination/reintroduction diet seriously: we are meant to eat as many foods as possible. Variety is key when healing the immune system. 

Some well-known elimination protocols include the Autoimmune Paleo diet or the Institute for Functional Medicine’s Elimination Diet. 

Miscarriage and autoimmune disease 


Sadly, miscarriage and autoimmune disease are also closely connected. If you have suffered multiple miscarriages, it is reasonable to ask your healthcare providers to investigate for autoimmunity or how your autoimmune diagnosis might be contributing.

Diagnoses of untreated celiac disease, antiphospholipid syndrome, systemic lupus erythematosus, undifferentiated connective tissue disease, and thyroid autoimmunity (Graves’ disease or Hashimoto’s) may lead to more miscarriage susceptibility than other autoimmune diseases. 

How are they connected?


Based on recent research, the link between miscarriage and autoimmune disease isn’t straightforward and is somewhat controversial. 

However, we know that certain autoantibodies can negatively interact with the placenta, the embryo, the mother’s hormonal balance, and the function of the immune system as it communicates between the mother and the fetus (12). More than likely, one or often a combination of these forces lead to miscarriage.

Up to 50% of women with untreated coeliac disease experience miscarriage or an unfavorable outcome of pregnancy. In most cases, after 6-12 months of a gluten free diet, no excess of unfavorable outcome of pregnancy is observed. The prevalence of undiagnosed coeliac disease among pregnant women is not known” (13) 

Practical steps


Finding an experienced physician and following the nutritional recommendations above apply to strengthening the body and reducing the risk of miscarriage, too. 

However, each autoimmune diagnosis is approached differently for preparation and support during pregnancy (14). So, it is especially critical to work with a clinician during preconception and pregnancy to get the specific guidance needed for your unique condition. 

Again, pairing this care with holistic care can be a fantastic route. A well-researched nutritionist or health coach can make dietary, lifestyle, and nutrient recommendations. For instance, the testing and therapeutic use of vitamin D may benefit pregnant people with an autoimmune diagnosis who experience recurrent pregnancy loss (15). 

Pregnancy complications and autoimmune disease

Autoimmunity can sometimes lead to complications during pregnancy, as well. 

The most commonly recognized issues are fetuses that are small for gestational age, low birth weight, and preterm birth. However, preeclampsia, characterized by heightened blood pressure and swollen hands and feet, autoantibody harm to the fetus, and stillbirth can also occur. 

How are they connected?


As stated above, some pregnancy complications are common for all autoimmune diagnoses. Others, however, are unique to the person and their specific disease. Ultimately, it is incredibly important to work transparently with your care team to determine your risk factors and mitigate any foreseeable risks to you or your baby.

When a fetus is small for gestational age or born with a lower-than-average birth weight, it is often the result of autoantibody/antigen complexes. These groups of immune cells alter the function of the placenta and can block essential nutrients from reaching the fetus. The outcome of fewer nutrients is a smaller baby (16). 

Immune cytokines can also play a role in this phenomenon. Cytokines are the messengers of the immune system, functioning similarly to hormones in the endocrine system. Some cytokines are inflammatory and can affect the placenta or the fetus. 

Rheumatoid arthritis and systemic lupus erythematosus are two autoimmune diseases linked to cytokine complications. While many babies can catch up on growth and neurodevelopment by about two years of age, it’s important to be aware that these particular diagnoses are also linked to an increased risk of autism spectrum disorder in the offspring (17, 18, 19, 20).

Practical steps


The best solution to avoid the risk of pregnancy complications is to work with your healthcare providers before conception to lower inflammation, autoantibody levels, and, if possible, disease severity. Steady control of symptoms and inflammation will mean a lower chance of issues for you and your baby. 


One way to reduce disease severity is an examination of lifestyle. Food and nutrients are radically important when navigating conception and pregnancy with an autoimmune disease. But finding ways to reduce stress and incorporate movement into the day is just as critical…yet easily overlooked. Stress has a mental and emotional toll, but it has a physical one, as well (21). What can you do in your day-to-day life to reduce stress or your reaction to it?

Pregnancy’s effect on autoimmunity


While we most often consider the links between infertility, miscarriage, and autoimmune disease, autoimmunity and pregnancy are not a one-way street. There is a bi-directional effect between pregnancy and autoimmune activity.

While certain diagnoses sometimes improve with pregnancy, such as rheumatoid arthritis and multiple sclerosis, others may worsen, such as thyroid autoimmunity or lupus. Why is this? 

How are they connected?


The immune and endocrine systems are intimately connected, to the point that some clinicians and researchers think that they are, in many ways, the same system!

The extreme hormonal shifts that happen in pregnancy correspond with immunological changes. The normal balance of the immune system is skewed by pregnancy, and autoimmune diseases respond accordingly. The changes quell some autoimmune diseases but flare others. Technically, these balances are controlled by hormones, cytokines, and the Th1/Th2/Tregulatory balance of the immune system. 

Amazingly, other physiological functions may contribute, such as metabolism and the nervous system (22). 

Practical steps


We can again rely on the usefulness of an anti-inflammatory diet and lifestyle. However, working with a very experienced nutritionist or herbalist to get specific and safe supplement or herbal recommendations may ease autoimmune symptoms during pregnancy. 

We must repeat: the experience and clinical knowledge of the practitioner is paramount when working with autoimmunity and pregnancy. Some herbs and nutrients can be detrimental during this time, both for the mother and the baby. 

However, the right compounds expertly used can create immune balance, pose no harm to the parent or baby, and create a lot of relief. 




  1. https://www.scientificamerican.com/article/the-terrible-toll-of-76-autoimmune-diseases/ 
  2. https://www.niehs.nih.gov/health/topics/conditions/autoimmune/
  3. https://pathology.jhu.edu/autoimmune/prevalence 
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966302/ 
  5. https://pubmed.ncbi.nlm.nih.gov/19772806/ 
  6. https://pubmed.ncbi.nlm.nih.gov/21239747/ 
  7. https://pubmed.ncbi.nlm.nih.gov/28277353/ 
  8. https://www.accessdata.fda.gov/drugsatfda_docs/label/2016/008085s066lbl.pdf 
  9. https://pubmed.ncbi.nlm.nih.gov/31837981/ 
  10. https://www.frontiersin.org/articles/10.3389/fcell.2022.713650/full 
  11. https://academic.oup.com/humupd/article/14/4/359/639610 (bidirectional effects paper)
  12. https://www.frontiersin.org/articles/10.3389/fendo.2022.873286/full#B37 
  13. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1727862/ 
  14. https://www.merckmanuals.com/home/women-s-health-issues/pregnancy-complicated-by-disease/autoimmune-disorders-during-pregnancy
  15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986007/ 
  16. https://www.clinicaladvisor.com/home/features/autoimmune-disorders-complicate-pregnancy/ 
  17. https://ped-rheum.biomedcentral.com/articles/10.1186/s12969-022-00667-w 
  18. https://pubmed.ncbi.nlm.nih.gov/29183859/ 
  19. https://pubmed.ncbi.nlm.nih.gov/26315754/
  20. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373490/ 
  21. https://www.frontiersin.org/articles/10.3389/fimmu.2020.01823/full 
  22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045787/