What Causes Hashimoto’s?

This article is the second in a series of three articles all about Hashimoto’s disease. It will cover what causes Hashimoto’s – the root causes and triggers. Check out the other two articles here:

Major credit to Dr. Isabella Wentz, PharmD for her 2017 book Hashimoto’s Protocol (and her earlier eBook The Root Cause). Her work summarizes an enormous amount of information about Hashimoto’s and clarifies current understanding of this disease.

Her book, the teaching of Dr. Alan Christianson, ND in his Healing Hashimoto’s training, several other courses I’ve completed over the past 10 years, plus my own clinical experience with my patients have shaped how I evaluate and treat Hashimoto’s in my practice.

“Quick! Name the Principles of Naturopathic Medicine!”

That was the first thing Dr. Helena Ovens, ND (RIP) asked me the first time I shadowed her in practice. And yes, she ordered me to do it quickly! Apparently I was one of the only students who actually listed them correctly. Because I did, we started out on the right foot to become friends and colleagues. I’ve always remembered this and have realized how important it is to keep these principles in mind!

Why are these Principles important for understanding what causes Hashimoto’s? Because three of them are key to understanding the way that Naturopathic Doctors view and treat chronic conditions like Hashimoto’s:

Identify and Treat the Cause (Tolle Causam)

Your Naturopathic Doctor’s primary goal is to determine and treat the underlying cause of disease.

Dog with magnifying glass over left eye

While symptom management is valuable, understanding the underlying CAUSE behind symptoms can lead to long-term improvement and greater resolution. This is where the power of Naturopathic Medicine shines!

A combination of conditions must exist to develop Hashimoto’s, including one or more triggers. Understanding these conditions and pinpointing your triggers makes it possible to create a treatment plan personalized for you.

The Healing Power of Nature (Vis Medicatrix Naturae)

Your Naturopathic Doctor works to restore and support the powerful and inherent healing abilities of your body, mind, and spirit and to prevent further disease from occurring.

One of the two Core Beliefs that drive my practice is the “Innate ability to heal.” Each of us is a collection of intertwined systems that constantly seek balance. Once we address underlying causes of disease/dysfunction (see above) and establish a nurturing environment, our body can regulate itself to resolve and prevent illness with less external intervention.

In Hashimoto’s cases the autoimmune attack on the thyroid gland can be minimized through appropriate treatment. This allows healthy thyroid function to be maintained much more easily.

Disease Prevention and Health Promotion

Your Naturopathic Doctor applies the above principles in a proactive form of disease prevention and health promotion.

Two hands clasped together

Treating the root cause and restoring the body’s innate ability to heal can resolve current health issues and prevent many future health issues.

Hashimoto’s is an autoimmune disease. The antibodies produced cause damage to the thyroid gland that can lead to permanent loss of function. Plus, having one autoimmune disease puts you at increased risk of developing other autoimmune diseases. Addressing the causes and triggers of Hashimoto’s can preserve thyroid gland function and prevent future disease.

What causes Hashimoto’s?

Hashimoto’s disease is an autoimmune condition and, as Dr. Isabella Wentz, PharmD explains in her book Hashimoto’s Protocol, autoimmunity develops when three conditions come together:

  1. Genetic susceptibility
  2. Intestinal permeability
  3. Triggering factor(s)

You need all three conditions! Having only one is not enough to develop an autoimmune conditions. By the way, that means that if you have an autoimmune disease, intestinal health is relevant to you EVEN IF you don’t have severe digestive symptoms.

What’s in your Genes?

Most people assume that your genes are “written in stone” and cannot be changed. However, there is the genetic CODE (which does not change) and whether that genetic code is expressed or silenced.

Did you know that even identical twins (who share the exact same genetic code) only BOTH develop Hashimoto’s HALF of the time? This means that if one twin has Hashimoto’s, the other only has a 50% chance of developing the disease.

Your environment has a profound impact on how genes are expressed. HOW you live can determine whether the genes that make a particular disease more likely become expressed. This is great news! Even though you can’t change your genetic code, you can exercise some control over your genes.

What is Intestinal Permeability?

Pay close attention here! Intestinal permeability (also known as “leaky gut”, probably because that is shorter and sounds a lot cooler) is (along with insulin resistance as discussed above!) one of the MOST IMPORTANT health issues facing the majority of adults in developed countries. And it is especially important for healing autoimmunity since WITHOUT this factor, autoimmunity cannot develop!

Our intestinal lining should be highly selective about what it allows to pass into our bloodstream, like a very good security guard. Intestinal permeability occurs when the normally tight barrier of our intestinal lining becomes compromised. An unhealthy intestinal lining becomes permeable, allowing undigested food, bacteria, viruses, fungus/yeast, and toxins to get through to places they don’t belong. This can lead to issues with digestion, immune function, and chronic inflammation.

A leaky gut changes the way the immune system regulates itself and can lead to autoimmunity under the right conditions. In most cases, intestinal permeability precedes the development of autoimmunity.

What Triggers Hashimoto’s?

If you have Hashimoto’s, then we already know you have genetic susceptibility AND intestinal permeability. Congratulations!?

Thankfully there are certain lifestyle changes that can help your body silence the genes for Hashimoto’s. Through Naturopathic treatment we can work on healing intestinal permeability which helps your immune system to regulate itself correctly (and stop attacking the thyroid gland).

However, when seeking to understand and correct what causes Hashimoto’s, the most profound healing occurs when we ALSO identify and correct your specific triggers for Hashimoto’s! This is where things get really interesting but more complex because these triggers are not the same for everyone. AND, this is where Naturopathic Medicine really shines.

There are MANY possible triggers for Hashimoto’s. Dr. Isabella Wentz, PharmD has done amazing work researching the possible triggers for Hashimoto’s and addresses them in four main categories in her book Hashimoto’s Protocol. Below, I’ve listed those categories PLUS an extra fifth category (that Dr. Wentz has also written about on her website) regarding hormones/estrogen as I see this often in my practice.

Remember that for most patients, there will be multiple triggers. It is not always easy to determine with certainty which triggers are relevant to you. In my practice I use your current symptoms, medical history, and questionnaires from the book Hashimoto’s Protocol to focus in on which triggers are relevant in your case.

1. Infections can trigger Hashimoto’s

This category of triggers is the most important to explore because there are many possible infections and it is difficult to treat without identifying what infection(s) are specifically relevant (or not!) in your case.

Under the right conditions and in some people, certain infections and/or the immune response you make can alter the way the immune system functions and lead to autoimmunity.

Unfortunately, it is not always possible to confirm whether you have or have had some infections. Thankfully, Dr. Wentz highlights five MAIN infections to examine first that are most often seen in patients with Hashimoto’s:

  1. Epstein-Barr virus
  2. H. pylori bacterial infection in the stomach
  3. Small Intestinal bacterial overgrowth (SIBO)
  4. Yeast/bacterial overgrowth in the large intestine
  5. Parasitic gut infections (most often Blastocystis hominis)

Did you notice that four of these five infections are of the DIGESTIVE SYSTEM? Infections in the digestive system can cause intestinal permeability (one of the necessary conditions to develop autoimmunity!) AND/OR intestinal permeability can cause you to be more susceptible to many infections…

I cannot stress enough how important it is to address digestive function in ALL cases of Hashimoto’s. Many patients with chronic digestive issues have overgrowth or flora imbalance. Correcting this leads to amazing results in so many health issues beyond digestion!

In addition to those top five, there are several other infections that have been associated with Hashimoto’s. These others are either less common or less strongly connected so the top five should be examined first.

2. Chronic stress and adrenal dysfunction can trigger Hashimoto’s:

This is the next most important area to investigate because in most cases of Hashimoto’s there is a component of chronic stress, whether physical, mental, or emotional. I don’t think I’ve seen a case of Hashimoto’s in which stress was NOT a factor. In some cases chronic stress can be the major trigger.

Your adrenals are small pyramid-shaped glands that sit on top of your kidneys. These little glands are actually powerhouses, producing all kinds of neurotransmitters and hormones that are essential for normal function.

One of the key hormones produced by the adrenal glands is cortisol, a stress hormone.  Did you know that cortisol decreases T3 (the more active thyroid hormone), increases auto-antibody production, and interferes with function of the thyroid gland?

Chronic stress means you are constantly flooding your body with cortisol, impeding thyroid function as well as setting you up for more disease down the road.  In fact, many hypothyroid symptoms (fatigue, depression, low libido, poor memory, weight gain) can ALSO be attributed to poor adrenal function as a result of chronic stress.

Supporting the adrenal glands and reducing stress is therefore a necessary part of any thyroid treatment and can improve efficacy of medication.

3. Food sensitivities can trigger Hashimoto’s


Remember how intestinal permeability (aka leaky gut) is one of the necessary conditions to develop autoimmunity?

Food sensitivities can contribute to AND be a result of intestinal permeability. Theses can be assessed via an elimination/challenge diet or blood testing.

The most common food sensitivity for patients with Hashimoto’s is gluten sensitivity (or celiac disease, which is a more severe manifestation). In most cases strictly eliminating gluten can improve thyroid function and reduce autoimmunity. In addition to gluten, other food sensitivities can contribute to Hashimoto’s, such as dairy, soy, eggs, nightshades, legumes, etc.

4. Toxins can trigger Hashimoto’s:


Someone in good health with optimal detoxification function can often handle “normal” exposure to toxins without major disruption to their health. However, if your health is compromised, toxin exposure can be a trigger for Hashimoto’s.

This is a huge category because we are exposed to SO MANY toxins on a daily basis! Here are some examples but this is not a complete list of toxins to consider if you have Hashimoto’s:

  • Bisphenol A and other plastics found in cooking materials, food storage, water bottles, and processed/fast foods
  • Teflon, aluminum, and other materials in cooking and food storage
  • Chlorine and fluoride in water
  • Household and personal care products (Check out the Environmental Working Group’s Home Guide, Guide to Healthy Cleaning, and Skin Deep Cosmetics Database to find out about the products you use)
  • Medications (such as Accutane, amiodarone, interferon/cytokine-based medications, lithium, tyrosine kinase inhibitors)
  • Mold
  • Toxic/heavy metals
  • Radiation, including dental x-rays
  • EMF sensitivity

5. Estrogen dominance can trigger Hashimoto’s

Flat rock with stones stacked on either side in balance, ocean in the background

As discussed above, the hormonal systems of the body are connected and can influence each other significantly.

Hormonal changes (such as pregnancy and perimenopause/menopause) are known to trigger Hashimoto’s. And, hormonal imbalance can also be a trigger for Hashimoto’s, specifically estrogen dominance.

What is “estrogen dominance”?

There is a strong connection between estrogen and Hashimoto’s. This may be one reason Hashimoto’s is so much more common in women compared to men. BUT, we all have estrogen and estrogen dominance affects men too!

Many of the fixtures of “typical” modern life (excess sugar/calories, processed foods, insulin resistance, exposure to toxins that disrupt hormones, lack of sleep, chronic stress, insufficient exercise) push us ALL toward estrogen dominance.

Estrogen dominance occurs when the balance between estrogen and progesterone is disrupted. This can occur for two reasons:

  1. Estrogen levels are high due to increased production, external sources of estrogen, or impaired detoxification pathways
  2. Progesterone levels are low (usually due to low production), so estrogen is relatively higher (dominant)

What encourages higher estrogen?

  • Medications (birth control, fertility treatments, hormone replacement therapy, etc)
  • Estrogen-mimicking substances also known as xenoestrogens (pesticides on food, plastics, personal care products, etc)
  • Increased body fat
  • Impaired detoxification

What encourages lower progesterone?

  • Chronic stress
  • Lack of sleep
  • Irregular or absent ovulation

Symptoms of estrogen dominance may include:

  • Premenstrual symptoms (irritability, headaches, tender breasts, etc)
  • Irregular periods
  • Fibroids, ovarian cysts, fibrocystic breasts, or other growths
  • Endometriosis
  • Acne
  • Headaches, migraines
  • Fertility problems
  • Insulin resistance
  • Autoimmunity

How does estrogen dominance trigger Hashimoto’s?

A relative excess of estrogen suppresses thyroid hormones and can trigger hypothyroidism. In addition, excess estrogen can specifically trigger Hashimoto’s by increasing thyroid antibodies.

Keep your eyes and inboxes open!

This article is the second in a series of three articles all about Hashimoto’s disease. If you haven’t read the first article yet, check out What is Hashimoto’s (and how to find out if you have it).

The third and final article is coming in the next couple of weeks and will cover how I treat Hashimoto’s in practice.


  1. Christianson, Alan. (2013). Healing Hashimoto’s Physicians’ Training.
  2. Wentz I. (2017). Hashimoto’s Protocol. New York, NY. HarperOne.
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