Top 10 Root Causes of Hashimoto’s (and what to do about it)

Table of Contents

• My Insane Journey to Uncover & Address the Root Cause of Hashimoto’s
• The Top 10 Root Causes of Hashimoto’s
• So, what causes Hashimoto’s?
  1. Intestinal Permeability, aka: Leaky Gut
  2. Nutrient Deficiencies
  3. Genetics
  4. Emotional Stress and Trauma
  5. Overtraining
  6. Mold Exposure
  7. Parasites
  8. Heavy metal exposure
  9. Gluten intolerance
  10. Hormone disruptors (xenoestrogens)
• So, how do you know what’s causing your Hashimoto’s?
• Want to work together on this?

Getting a Hashiomoto’s diagnosis can bring up all the emotions, including: fear, liberation (my symptoms finally have a name!), devastation, relief, shame (where did I go wrong? I’ve always been health-conscious), anger, and uncertainty.

It also brings up a lot of questions, the main one being: what caused this in the first place?

Unfortunately, too many of us get the same vague answers, like: 

“It’s an autoimmune condition where your body attacks your thyroid. We don’t know why. t’s genetic. There’s no cure, but here’s a prescription for medication to take for life.”

Or, if you’re lucky, a slightly more compassionate and informed answer, like: 

“It’s an autoimmune condition. It may be caused by genetics and environmental factors, but it’s not your fault. There’s no cure, but there are medications you can take to relieve symptoms. Getting off gluten may also be helpful.”

While both answers contain some truth, they don’t answer the burning question: “What is the root cause my Hashimoto’s?”

The second answer pretty much sums up the general medical consensus: the cause of Hashimoto’s Thyroiditis is unclear, but it’s probably a combination of genetics and environmental factors. New research also suggests certain viruses, like Hepatitis C, may play a role.[1]

But what if I told you research has shown there are many potential root causes of Hashimoto’s and hypothyroidism beyond just genetics that most doctors don’t talk about? 

And, even better, you have the power to put your Hashimoto’s into remission by addressing these root causes.

In this article, I’ll share the top ten root causes of Hashiomoto’s based on research, plus how to address them and reclaim your health.

My Insane Journey to Uncover & Address the Root Cause of Hashimoto’s

Before being diagnosed with Hashimoto’s, I was running a seven-figure clinic in New York City with a team of ten and was burning the candle at both ends.

Then in 2016, I had my first kiddo and had all the “new mom symptoms” like being exhausted, my hair falling out, not being able to lose weight, brain fog, and just not feeling like myself.

Everyone told me it was normal…but then it got worse.

At 18 months postpartum, I hit rock bottom.

I was in constant pain, struggling to finish sentences, gaining weight for no apparent reason, unable to complete normal workouts (and injuring myself constantly), and feeling like a shadow of my former self.

So, I saw a primary care doctor, an endocrinologist, and three functional medicine doctors before my third functional medicine doctor (the fifth doctor!) diagnosed me with Hashiomoto’s and helped identify the root causes. 

And thank GOD for her.

My root causes, which will give you a preview of what we’re about to cover, were:

• Undereating, specifically not eating enough protein first thing in the morning and throughout the day
• Food sensitivities to gluten and dairy
• Intestinal permeability (Leaky Gut Syndrome)
• Parasites from traveling in my twenties
• Mold exposure from my Brooklyn condo that we remediated twice

Over 9-12 months of addressing those root causes, my Hashimoto’s went into remission and stayed in remission throughout a second pregnancy, which is pretty rare.

Today, I’m still in remission, thanks to what I’ve learned (and what I now teach others) about addressing the causes of Hashimoto’s thyroiditis.

The Top 10 Root Causes of Hashimoto’s

I don’t know about you, but the worst thing a person could tell me is that I have a disease, and there’s nothing anyone can do to fix it.

I simply can’t accept that. And if you’re reading this article, I bet you feel the same.

That’s why, when I finally got my Hashimoto’s diagnosis, I dug deep into the research behind the triggers and hashimoto’s thyroiditis root causes.

I was also fortunate to find a functional medicine doctor who helped me further understand what causes this debilitating autoimmune disease and how to reverse it.

So, what causes Hashimoto’s Thyroiditis?

Spoiler alert: it’s not just one thing!

The most ground-breaking research on the root cause of Hashimoto’s and other autoimmune conditions comes from the research of Italian gastroenterologist Dr. Alessio Fassano.

Dr. Fassano is credited with many discoveries regarding gluten intolerance and autoimmune pathology (origins/root cause), including what’s known as “The Alessio Trifecta” or “Autoimmune Triad.”

According to Dr. Fassano’s research, the “trifecta” of Hashimoto’s autoimmune causal factors include three things [2]:

1. A specific genetic predisposition.
2. A physical, mental, environmental, or emotional trigger such as stress (physical, mental, emotional), certain medications, environmental toxins, pathogens, viruses, and/or an antigen or foreign substance that creates a prolonged immune response.
3. Intestinal permeability (also known as leaky gut).

Are the light bulbs and gut feelings starting to fire? Feeling like OMG, this is so me! 

Then, stick with me as we dive deeper into the underlying causes and triggers of Hashimoto’s.

1. Intestinal Permeability, aka: Leaky Gut

Intestinal permeability, commonly known as Leaky Gut Syndrome, is one of the top root causes of Hashimoto’s.

It’s also the reason many Hashi clients experience digestive health issues, which are also caused by leaky gut, creating a vicious cycle.

So, what is intestinal permeability?

In a nutshell, intestinal permeability occurs when the tight junctions in your gut expand and stretch to create microscopic holes.

Think of a healthy gut as a tightly woven net that only lets beneficial molecules, like nutrients, in while keeping larger molecules, like undigested food particles, pathogens, bacteria, and viruses out.

 In cases of intestinal permeability, that net is stretched out, allowing all kinds of foreign particles to enter.

This causes the immune system to go on red alert and crank up its inflammatory response to fight off these foreign invaders.

A heightened immune response is a good thing when you have an acute infection.

However, chronic heightened immune response causes chronic inflammation and (you guessed it) autoimmunity, like Hashiomoto’s, IBS, etc., over time.

Compromised gut barrier function can also impact nutrient absorption and lead to nutrient deficiencies such as iron and vitamin B12.

So, leaky gut is a leading cause of Hashiomoto’s but has its own list of causes, including poor nutrition, gluten or other food sensitivities, chronic stress, or unresolved gut infections.

Leaky gut is also a primary factor in the previously mentioned Alessio Trifecta: Leaky Gut + Genetics + Stress = Autoimmunity. 

This is why the best integrative functional medicine doctors start with gut health when addressing Hashiomoto’s and other autoimmune conditions.

2. Nutrient Deficiencies

I want to be careful here because too many women with undiagnosed Hashimoto’s have been told their symptoms are due solely to nutrient deficiencies.

So, they start on a specific nutrition and supplement protocol, feel a bit better…, and then tank again after a few weeks or months because the full spectrum of root causes has not been addressed.

As mentioned in the previous point, nutrient deficiencies do contribute to and may trigger Hashimoto’s. 

But, like an inquisitive three- or four-year-old, we must keep asking: Why? Specifically, why do I have nutrient deficiencies in the first place?

Autoimmune conditions, like Hashiomoto’s, make it harder to absorb the nutrients we eat (because processed foods rob us of nutrients, and nutrients are absorbed in the gut). 

In addition, the elevated autoimmune response creates a greater demand for nutrients.[3]

The fix: focus on nutrient-dense diet and take steps to heal and seal the gut.

Many people also benefit from supplemental zinc, B vitamins, magnesium, glutamine, and iron.

3. Genetics

There’s a saying in epigenetics (the science of gene expression): “Genes load the gun, and the environment pulls the trigger.”

In other words, genetics play a role in Hashiomoto’s risk, but they require an environmental trigger to be activated. 

Environmental trigger(s) may range from emotional trauma or stress to mold, heavy metals or certain medications and vary from person to person.

This explains why some people with a family history of Hashimoto’s develop the disease while others do not.

The takeaway: your genes are not your destiny! 

Research has shown that addressing physical, mental, emotional, and environmental triggers can help switch off genetic expressions that may contribute to Hashiomoto’s and autoimmunity, even if you have a genetic susceptibility.[4]

More on this to come.

4. Emotional Stress and Trauma

In my experience working with hundreds of Hashi ladies, emotional stress and trauma almost always play a role in the onset and progression of the disease.

This correlation has also been documented by various studies. [5, 6]

Yet, in my opinion, it is largely ignored or unaddressed in conventional medicine and even integrative medicine circles.[7, 8, 9, 10, 11]

For example, studies have shown stress negatively impacts:

• Digestive function
• Immune function and inflammatory response
• Gut barrier function
• Nutrient levels
• Hormonal balance
• Sleep cycle
• And much more

In my case, the stress of pregnancy, labor and delivery, and becoming a new (and very sleepless) parent played a significant role in the onset of my Hashimoto’s.

It wasn’t the only factor, but it’s what finally pulled the trigger.

Another prime example comes from a ground-breaking Swedish study titled: “Association of Stress-Related Disorders With Subsequent Autoimmune Disease,” published in Journal of the American Medical Association (JAMA).[6]

In this study, the researchers observed the effects of stress-related disorders on over 100,000 patients in comparison to over 1 million patients without stress-related disorders and over 100,000 siblings of the patients with stress-related disorders for approximately 32 years.[11]

Their goal was to assess the association between stress and autoimmune disease.

They concluded that those with stress-related disorders had a significantly higher associated risk of developing autoimmune disease compared to those without, including their siblings.

We also see evidence of this scientifically and clinically in the increased risk of hypothyroidism, postpartum thyroiditis, and Hashimoto’s following pregnancy, which is a beautiful and incredible, yet very physically, mentally, and emotionally stressful event. 

Especially in modern times when women have very little immediate and ongoing support.

On the other end of the spectrum, too many women are told their Hashimoto’s symptoms are “just from stress” and given antidepressants and anti-anxiety medication, which ignores the actual cause.

If someone tells you that having no energy, clumps of hair falling out, anxiety, dry skin, irregular periods, mood swings, trouble sleeping, and/or heart palpitations is/are just due to “stress,” that’s your cue to run, not walk, to get a second opinion.

5. Overtraining

Exercise is essential to attaining and maintaining optimal health, preventing disease, balancing hormones, and increasing longevity.

But…you can get too much of a good thing.

Specifically, over-training, especially in women and especially in women who are stressed out and have adrenal fatigue (known clinically as HPA Axis Dysfunction), can trigger the onset of Hashimoto’s.

While a moderate amount of exercise, like we teach in Thyroid Strong, helps keep your thyroid healthy and strong, too much creates an unhealthy stress response, which will wear you down over time.

It’s even worse if you don’t give yourself optimal recovery time and the fuel you need (aka, enough protein, vitamins, minerals, and healthy carbs) to rebuild muscle.

When we’re young, we can get away with doing double spin classes, lots of running, and hours of CrossFit. 

I did it because I was trying to lose the last 25 lbs of baby weight.

However, overtraining catches up with us as we get older, especially after having babies and nearing middle age.

How do you know if you’re overdoing it?

Symptoms like excess soreness (some soreness is good, especially when going up in weight or starting a new program, but you shouldn’t feel like you can barely move), fatigue, delayed recovery time, trouble sleeping, and feeling depleted versus energized after exercising are all telltale signs you’re overdoing it, girl.

Instead, I recommend focusing on functional movements with plenty of recovery time, like strength training with heavy weights, walking 8,000-10,000 steps daily, proper warm-ups, and fueling your body with enough protein.

Learn more in: 8 Tips For Exercising With Hashiomoto’s

6. Mold Exposure

Mold exposure greatly contributed to my Hashimoto’s journey, so much so that I moved several times, even leaving New York City for Colorado’s dryer climate.

Although I’m happy I made the move and am healthier for it, I couldn’t totally outrun the mold.

Since continuing to move isn’t feasible, the solution for me (and what I recommend to clients) is to be meticulous about keeping mold out of your home and enhancing your health to such a level that inevitable mold exposure won’t bring you down.

I’ve written a lot about mold (and will write more), but here are the cliff notes with links to learn more:

• Mold toxins disrupt thyroid function by blocking the activation of thyroid hormones, which impairs overall thyroid function.[11, 12]
• Mold is more common in homes, businesses, and schools than we think. 
• Toxic mold produces toxins known as mycotoxins, which can negatively impact overall health, including thyroid function. These species include:

• • Cladosporium
  • Penicillium
  • Fusarium
  • Aspergillus
  • Stachybotrys
• Symptoms of mold exposure can range from subtle to severe and may include:[14]
• Allergic reactions
• Anxiety/depression
• Autoimmunity
• Cognitive issues
• Fatigue
• Impaired detoxification
• Hormonal imbalance
• Lowered immunity
• Pain
• Reproductive health issues
• Skin issues like eczema
• Thyroid dysfunction
• Weight-gain
• Various “mystery” symptoms

Fortunately, you can recover from mold exposure by identifying and removing the source via relocating or remediation and working with a mold-literate doctor to regain your health.

Learn more in my Mold Exposure Masterclass

7. Parasites

Parasites are often ignored as a possible cause of Hashiomoto’s Thyroiditis, especially in first-world countries with clean water.

However, parasitic infections are extremely common and can cause or contribute to a leaky gut, which opens the doors for (you guessed it!) Hashimoto’s and other autoimmune conditions.

Parasites are also opportunistic when heavy metals, mold, or other toxins are in play. 

So you can see how these causal factors work together to create the “perfect” Hashimoto’s storm.

Now, when I’m talking parasites, I’m not only talking about tapeworms, hookworms, whipworms, or pinworms.

The most common parasite associated with Hashimoto’s is Blastocystis hominis, but we see many others on labs.

Stool testing is typically what we use to identify these little buggers. And evicting them is relatively straightforward once we know what we’re working with.

Full disclosure: with due respect, most conventional MDs aren’t trained to look for parasites, and some don’t even acknowledge that they can cause a problem. Most will say “we don’t have parasites here in the States.”

Fortunately, pioneering integrative physicians and practitioners have been helping people restore their health by identifying and addressing parasitic infections for years.

And yes, typically, you can get rid of them naturally using specific herbs, supplements, and integrative therapies like enemas and colon hydrotherapy.

Get more information on addressing parasites and healing gut infections in my: Stealth Gut Infections & Hashimoto’s Masterclass

8. Heavy metal exposure

Heavy metals are ubiquitous in our environment. From soda cans to dental fillings, food to water, it’s impossible to avoid these toxins.

So, why do they bother some people and not others?

Well, a healthy body can detoxify a lot of junk, including some levels of heavy metals.

However, even the healthiest individual would be hard-pressed to detoxify the sheer quantity of metals we are exposed to in the twenty-first century. And these accumulate with age.

For example, heavy metals like aluminum, lead, and mercury are neurotoxic, endocrine-disruptors, and have been shown to disrupt thyroid function.[15, 16, 17, 18]

Unfortunately, “the general consensus” is that sure, heavy metals are super toxic, but most people aren’t exposed to enough to cause a problem.

Myself and many other experts would challenge that consensus based on what tests have revealed about levels of heavy metals in baby formula and baby food alone! [19, 20]

Additional reports show that tap water, bottled water, and various foods, supplements, and medications also contain a concerning amount of heavy metals, far beyond the “safe range” set by the FDA and other governing bodies. [21, 22, 23, 24]

The FDA also now recognizes mercury amalgam fillings may be harmful for women who wish to become pregnant, pregnant women, nursing mothers, children, and others.[25]

Plus, many pesticides and herbicides used on our foods are heavy-metal-based, which means we are exposed through our food, water, air, and soil.

As mentioned previously, we also know that heavy metals can disrupt endocrine, thyroid, brain and a host of other biological functions.

So, it’s not exactly a stretch to suggest heavy metal toxicity may be negatively impacting our health (and triggering thyroid dysfunction).

When we address this by eliminating or reducing everyday exposures (water, food, immediate environment) and through safe heavy metal detox protocols, people get healthy, and thyroids get happy!

Reducing heavy metal load is also essential for recovering from mold exposure, leaky gut, and parasite infections. It is a causal or contributing factor that cannot be ignored.

If you’ve tried everything and have been unable to move the needle with your symptoms, I strongly suggest getting your heavy metal levels checked by an informed and experienced doctor.

I talk about this more in: The Best Water Filter For Hashiomoto’s

9. Gluten intolerance

Gluten is one of the key factors in the Alessio/Autoimmune Trifecta because it contributes to intestinal permeability.

How does this work?

Dr. Fasano discovered it’s due to a protein called zonulin, which is released in response to harmful bacteria and gluten.[26]

Zonulin is an inflammatory protein that temporarily opens up tight junctions in the gut to flush out harmful bacteria (think diarrhea). 

This helps fend off things like E. Coli or Salmonella.

However, too much zonulin in response to regular gluten consumption causes the tight junctions to remain open to pathogens and undigested food particles, leading to intestinal permeability and autoimmune conditions like Hashimoto’s.

So, why can some people eat gluten and not get sick?

Dr. Fasano’s work has shown that gluten-sensitive individuals’ zonulin levels tend to be higher. Meaning they either can’t break it down normally or their bodies excrete too much every time they eat gluten.

I would also add that many people are gluten-sensitive or intolerant (think gas, bloating, indigestion, food intolerance, brain fog, or fatigue after eating, etc.) and don’t even realize it.

Additional research has shown a gluten-free diet can help with autoimmune conditions, including Hashiomoto’s.[27]

I’ve been gluten-free for years now, and I suggest the same to all my Hashi clients.

It’s not that difficult to cut gluten these days, and it’s one of the easiest and most affordable ways to help heal your gut and your thyroid.

10. Hormone disruptors (xenoestrogens)

Our modern world is rife with hormone-disrupting chemicals.

I don’t want to create paranoia, but they’re in our food, household products, cleaning products, toys, plastics, medications, pesticides and herbicides, fragrances, receipts and paper products, pots and pans, outdoor gear, and many other places.

Heavy metals are also considered endocrine disruptors.

Regarding thyroid function, xenoestrogens (xeno meaning foreign) are a girl’s worst friend.

These synthetic chemicals found in things like phthalates, which are prevalent in plastics and fragrance, and PFASs, also known as forever chemicals used in non-stick chemicals, mimic the effects of natural estrogen in the body, resulting in a “fluster cluck” of hormonal imbalances.

To be clear, natural estrogen is a really good thing for women. 

We need it for everything from cognitive function and bone density to immunity, sexual, and reproductive health.

But, xenoestrogens disrupt this delicate hormonal balance, which also affects thyroid hormone levels.

This is why it is so crucial for Hashi ladies to adopt a low-tox lifestyle to reduce exposure to these types of chemicals in the home.

A great place to start is by going completely fragrance-free in household, cleaning, laundry, and personal care products.

For next steps, switch from plastic food storage containers, water bottles, and bags to glass or silicone, buy natural, low-tox cleaning and personal care products rated 1-2 on EWG Skin Deep App, and (when you’re ready) get rid of all non-stick cookware in favor of cast iron, stainless steel, or enameled cast iron and installing a high-quality water filter to filter out endocrine-disruptors in water.

You don’t have to do everything all at once. Baby steps are fine. But start somewhere, like with those heinous endocrine-disrupting fragrances, and go from there.

So, how do you know what’s causing your Hashimoto’s?

As you now know, there are many potential root causes of Hashimoto’s, and they’re often layered.

The best way to get to the bottom of your Hashimoto’s is to work with a functional medicine doctor or practitioner who understands how to test for these root causes.

Excellent functional labs are available for most of these causes, but most doctors are unaware of them or how to interpret them.

This information will help you and your doctor or practitioner prioritize where to start and how to begin detoxing and rebuilding safely and effectively.

Want to work together on this?

Helping women address the root cause of Hashimoto’s and thrive is my passion, and has been since I reversed my Hashimoto’s and started Thyroid Strong in 2018.

I’m excited to announce I’m accepting a limited number of clients for my one-on-one functional health coaching for Hashimoto’s.

In this program, we’ll work together through coaching calls and labels to get to the root cause(s)of your Hashimoto’s, address it/them using a custom functional medicine approach, and rebuild your body to its highest level of strength and resilience.

Click here to learn more about one-on-one health coaching, and I look forward to working with you!

Stat Strong,

Dr Emily Kiberd