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Written by
Kayla Matthews
Medically Reviewed by
Dr. Anshul Gupta

An autoimmune disease develops when your body fails to distinguish between itself and foreign invaders it needs to attack. Approximately 1 in every 20 people worldwide has an autoimmune disease. Some diseases develop most commonly during childhood, others in early adulthood, and some develop later in life. Experts have identified more than 80 unique autoimmune diseases, many of which are lifelong conditions. (Source, Source)

There are two types of triggers to consider in autoimmune diseases — those that bring about disease development, and those that trigger flares. In this article, we’ll look at both.

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What Causes Autoimmune Diseases?

Scientists don’t know what causes autoimmune diseases, but some people are more likely to develop them. For example, there’s a genetic component, which means a person with certain inherited traits or genes from their family may be more likely to develop an autoimmune disease. (Source)

Beyond that, some autoimmune diseases are more prevalent among specific groups. Overall, autoimmune diseases are most common in women. There are also significant variations between different ethnicities. African Americans, for example, are more likely than European Americans to develop systemic lupus erythematosus (SLE) but less likely to develop type I diabetes or multiple sclerosis (MS). (Source)

So, why do some people with dispositions develop autoimmune diseases while others don’t? There’s evidence that viruses, bacteria, hormonal changes, stress, drugs, toxins, and some lifestyle factors can trigger autoimmune diseases in people who are at risk. (Source, Source)


It’s widely accepted that viral infections are a major factor in the development of autoimmune diseases. However, the connections between the two are poorly understood.

One theory is that antigens (substances that trigger an immune response) within the viruses may be similar in shape and size to molecules within the body. It’s possible this phenomenon, termed “molecular mimicry,” may confuse the body, so it begins attacking itself.

Alternately, some experts have proposed something called “bystander activation,” where the immune system overreacts to a viral infection, triggering inflammation in a specific area of the body and initiating the release of the body’s own antigens, which the immune system attacks. (Source)


Regardless of your autoimmune status, your body is full of bacteria. Some bacteria are good and help you stay healthy, but others are harmful and can make you sick. Your gut microbiome consists of trillions of microorganisms in your gut, including bacteria.

Immune dysfunction can be triggered by changes in the gut microbiome. The inflammatory bowel diseases Crohn’s and ulcerative colitis, for example, are characterized by abnormal growth of a specific type of gut bacteria called proteobacteria. (Source)

A well-functioning body depends on balance, and it’s not just too many bacteria that can cause problems. Antibiotic use can disrupt the balance within the gut microbiome, potentially triggering autoimmune diseases. (Source)

a pregnant belly

Hormonal Changes

Events characterized by major hormonal changes, such as pregnancy, can lead to the development of autoimmune diseases. The influence of hormones on autoimmunity partly explains why women are more affected than men.

Women undergo drastic hormonal changes at puberty and again at menopause. As noted, in women with children, there’s another boost in activity during pregnancy. Estrogen, progesterone, androgens, leptin, oxytocin, and prolactin (all hormones that can increase or decrease in concentration) play roles in the body’s immune response. (Source)

Pregnancy doesn’t just trigger the development of autoimmune disease in the moment, either. There’s evidence that having a pregnancy can increase a woman’s risk of developing an autoimmune disease decades later. (Source)

Environmental Factors

Environmental factors play a role in immunity. Cigarette smoke, pesticides, mercury, silica, and other substances we commonly come into contact with have been linked to the development of autoimmune diseases. (Source, Source)

a person with their eyes closed and smoke in their face


Stress is strongly associated with a range of negative health outcomes. Some conditions are stress-induced, meaning stress causes them. Others are stress-aggravated, which means stress can make them worse. In the case of autoimmune diseases, it seems stress (both physical and emotional) may trigger or worsen certain conditions. (Source, Source)

Poor Sleep

Sleep has a restorative effect on immune processes. There’s evidence that long-term lack of sleep (or poor quality sleep) could lead to the development of autoimmune diseases. Interestingly, there’s also evidence that the sleep disorder narcolepsy may be rooted in autoimmunity, indicating there are many connections between autoimmunity and sleep that we don’t yet understand. (Source)

What Triggers Autoimmune Flares?

For many people with autoimmune diseases, symptoms come and go. If you have an autoimmune disease, you likely experience alternating periods of remission (where your symptoms aren’t noticeable) and flares. Many of the things that bring about the development of autoimmune diseases also exacerbate symptoms and trigger flares.

a pregnant women holding hands with her young child

Hormonal Changes

Disease status is closely linked to hormonal status, with direct relationships between the two.

It’s not clear why, but type I diabetes risk increases when menstruation — marked by significant changes in the levels of several hormones — starts at an age that’s younger than average.

Pregnancy is associated with an increase in SLE flares due to increased estrogen, and MS usually gets worse after delivery.

Women who experience menopause at a younger age face a higher risk of certain type I diabetes complications, and they often experience more severe MS symptoms and struggle with worsening psoriasis.

It’s worth noting that pregnancy reduces the severity of joint pain and flares in many women with rheumatoid arthritis and psoriasis. Interestingly, the spike in estrogen is protective in women with those particular conditions. (Source)

In their review of relevant literature, one team of researchers found that between 13.5% and 65% of women with SLE experience a flare during pregnancy. In 15% to 30% of the women who experience them, the flares severely impact the kidneys or other organs. (Source)


Stress weakens your body’s defenses, regardless of whether or not you have an autoimmune condition. Unfortunately, the relationship between stress and autoimmune symptom severity is bidirectional. Stress can trigger a severe flare, and a severe flare can increase stress levels. (Source)

In a study of people with spondyloarthritis (a kind of arthritis that affects the spine and large joints) and rheumatoid arthritis, stress was among the most commonly cited triggers of flares, with participants often reporting flares following periods of exceptional stress. (Source)

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Poor Sleep

Many of the functions within your body that contribute to poor sleep and fatigue also contribute to inflammation. Likewise, many of the conditions associated with fatigue, such as anxiety and depression, are also associated with autoimmune diseases. (Source)

An assessment of studies looking at the connections between sleep disturbances and inflammatory bowel disease (IBD) points out that the best way to manage a condition with no cure (such as IBD) is to try and prevent flares. The researchers conducting the assessment found that circadian clock genes (the ones that regulate your sleep/wake cycle) influence the permeability of the intestinal lining. This permeability is also associated with autoimmune flares, so while more research is needed to fully understand the impact of sleep on autoimmune flares, the link between the circadian clock genes and gut permeability may play a role. (Source)

Pollutants and Toxins

Air pollution comes from both human-made and natural sources. Its negative effects are well known. Air pollution is linked to cancer, cardiovascular and respiratory diseases, and more. Because of its associations with oxidative stress (in which metabolic byproducts cause cell and tissue damage) and inflammation, the National Institute of Health (NIH) has identified a need for research to explore the connections between air pollution and immune system disorders. (Source)

In a study of over 20,000 people with various autoimmune diseases, researchers found that those exposed to short-term air pollutants were more likely to seek frequent changes in treatments to improve their conditions. This suggested that those exposed experienced more frequent and more severe flares than those who weren’t exposed. (Source)

There’s growing evidence that pesticides and herbicides used on foods can influence the immune system’s functionality, which may lead to the worsening of autoimmune symptoms. (Source, Source)

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Dietary Choices

Nutrition is a complicated topic that becomes exceedingly complex when you add in autoimmune diseases. Many publicly-available resources exist for people with average needs, but unfortunately, what’s healthy for someone without an autoimmune condition is not necessarily ideal for someone with one.

In a study of 145 people with IBD, 28% felt they were sensitive to gluten. A survey of people with IBD found that the majority of participants who tried a gluten free diet saw improvements in their gastrointestinal symptoms. (Source, Source)

People with irritable bowel syndrome (IBS) may benefit from a low FODMAP diet. In an assessment of relevant studies, a research trio from the Netherlands found that scientists commonly point to a low FODMAP diet as an effective way to reduce symptoms and improve quality of life in people with IBS. Having an autoimmune disease makes it more likely you will develop IBS, and limiting FODMAPs may help reduce intestinal inflammation. (Source)

In general, people with autoimmune diseases benefit from the autoimmune protocol (AIP) diet. In a study of 16 women with Hashimoto’s thyroiditis, most participants saw significant improvements in symptoms (including joint pain and muscle aches) within 4 weeks. (Source)

Your ideal diet is unique to you. To help pin down which foods work for you (and which don’t), we recommend working with WellTheory’s team of qualified, specialized Nutritional Therapy Practitioners and Health Coaches who can build a fully-customized care plan to meet your specific needs.

Illnesses and Injuries

Certain illnesses and injuries can trigger autoimmune flares. Illnesses, even ones that are short-lived, such as the seasonal flu, challenge your immune system. As a general rule, anything that strains your immune system may trigger an autoimmune flare.

A research team in Korea studied national insurance data on patients with SLE who became infected with influenza. They found that influenza infection increased the risk of a flare (or several flares) in both men and women and in all age groups. Additionally, they found a significant association between influenza infection and severe flares requiring hospitalization. (Source)

Research shows that injuries can trigger psoriasis flares on healthy sections of skin in people who have the condition. Doctors call this finding the Koebner phenomenon, and it may occur after an injury in as many as 30% of people with psoriasis. (Source)

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Tips on Avoiding Triggers to Prevent Autoimmune Flares

Understanding your triggers can empower you to regain control of your autoimmune disease. While triggers vary from person to person, there are steps you can take to potentially reduce the frequency and intensity of your flares.

  • Find a diet that works for you, and stick to it. There are a number of mechanisms supporting the use of the AIP diet to improve symptoms and reduce flares. This diet is safe for most people.
  • Prioritize sleep. Needs vary, but the National Sleep Foundation recommends 7 to 9 hours each night for adults aged 18 to 64. Children and teens need a little more, and older adults need a little less.
  • Engage in stress-busting activities and practices. Many people, including those with immune disorders, benefit from mindfulness-based stress reduction techniques.
  • Reduce your exposure to toxic pesticides and herbicides by choosing organic foods when it’s possible and reasonable to do so.
  • Monitor your air quality and use an indoor air cleaner if needed to reduce the impact of primary pollutants on your body.

(Source, Source)

The Bottom Line on Triggers for Autoimmune Diseases

We don’t know what causes autoimmune diseases, but genetic factors and a variety of lifestyle factors can contribute to disease development. Many of these same risk factors can also trigger autoimmune flares in people who already have an autoimmune disease.

If you’re struggling with disruptive flares — eating well, sleeping well, managing your stress levels, and reducing your exposure to toxins may help reduce the impact of your condition. If you're looking for accountability and support in making lifestyle changes that will reduce your symptoms, consider becoming a WellTheory member and you'll get paired with a Care Team who will create a personalized care plan perfect for your particular health goals.

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Rheumatoid Arthritis
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Triggers for Autoimmune Diseases — What You Need to Know

Awareness of potential triggers may reduce your risk of developing an autoimmune disease, and help prevent flares if you already have one.
Medically Reviwed
Written by
Kayla Matthews
Medically Reviewed by
Dr. Anshul Gupta
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