A Functional Medicine Approach to Hashimoto’s Thyroiditis and Hypothyroidism

What is Hashimoto’s Thyroiditis

Hashiomoto’s thyroiditis is an autoimmune disease that, over time, destroys thyroid tissue and causes hypothyroidism. It is the most common cause of hypothyroidism in the U.S. and affects a surprising number of people (mostly women) worldwide. Some sources say it is 10 times more common among women than men, and most are diagnosed when they are between 30 to 50 years old.1

Likely if you receive this diagnosis, you will be treated with a thyroid medication called Levothyroxine, but not much will be done to address the autoimmune component of the disease. Fortunately, there are solutions, and this is a condition I treat regularly in my functional medicine practice. And as a thyroid patient myself, I can attest to the importance of not only addressing thyroid hormone replacement but also addressing the immune system component of this disease.

In this article, you’ll learn what’s behind Hashimoto’s, and how a functional medicine approach can help you prevent, detect, and treat its underlying causes.

Why Hashimoto’s is so Commonly Underdiagnosed

Autoimmune diseases, like Hashimoto’s, can be tricky to diagnose and treat for a few reasons.

#1: Symptoms of Hashimoto’s are nonspecific and can seem unrelated.

#2: If hypothyroidism is suspected, generally a TSH is the only lab that is drawn. However this approach has significant limitations and may exclude a large subset of patients, resulting in the potential misdiagnosis of hypothyroidism.2 This is best summarized in the Journal of Thyroid Research:

“While this approach has been successful in many ways, it has some grave limitations. This includes the basic question of what constitutes an agreed reference range and the fact that the population-based reference range by far exceeds the variation of the intraindividual set point. Both problems result in a potential misdiagnosis of normal and pathological thyroid function in a substantial proportion of patients.”3

#3: Basic lab work doesn’t test for autoimmune conditions, like Hashimoto’s. You need advanced lab panels to accurately detect this condition and determine its causal factors.

Hashimoto’s Symptoms

First of all, it’s important to remember that Hashimoto’s is a problem with the immune system. Over time the autoimmune destruction of the thyroid gland can also create a problem with low thyroid function. Early in the disease patients may also experience intermittent symptoms of hyperthyroidism.4

Thus some patients may experience many of these symptoms while others experience only one or two. Much of this depends on how well you take care of your health and where you are in the disease progression.

Those of us with Hashimoto’s can experience a wide range of symptoms which might include:

  • Anxiety
  • Bloating
  • Depression
  • Digestive issues
  • Fatigue
  • Feeling like you can never get enough sleep
  • Hair loss
  • Irregular periods
  • High cholesterol or blood sugar
  • Hormonal issues
  • Infertility
  • Insomnia
  • Joint pain/body aches
  • Lack of motivation
  • Lowered immunity/greater susceptibility to colds, viruses, etc.
  • Low libido
  • Miscarriages
  • Mood swings
  • Palpitations
  • Skin issues
  • Trouble focusing
  • Weight problems (typically weight gain or trouble losing weight)

This is by no means an exhaustive list, but it gives a good overview of how vast (and nonspecific) the symptoms can be.

How to Detect Hashimoto’s in Lab Testing

If I suspect Hashimoto’s or a thyroid problem in a patient, I order the following lab work:

  • TSH—this is an indirect (but specific) measure of thyroid function. Essentially TSH measures how the pituitary gland (in the brain) is communicating with the thyroid. When high it is indicative of hypothyroidism.
  • Free T4—T4 and T3 are your body’s main thyroid hormones. Free T4 measures the bioavailable (unbound) hormone produced by the thyroid gland. Low T4 is a marker of low thyroid function.
  • Free T3—T4 is converted to T3 in the peripheral tissues. Free T3 is also known as the “gas.” A low level of T3 can indicate low thyroid function, or just a problem with conversion. Conversion issues are quite common with my patients, especially those with a lot of stress, inflammation, or high toxic burden. According to the American Thyroid Association “measurement of free T3 is possible, but is often not reliable and therefore not typically helpful.”5 Clinically I find this lab to be very useful, but it is significantly impacted by the timing of the lab draw.
  • Reverse T3—some T4 is also converted to reverse T3. Reverse T3 is also known as the “brakes.” High levels of reverse T3 can be responsible for symptoms of hypothyroidism, since it competes with free T3 for cell receptor sites. However, this is generally not a problem with the thyroid, but rather a sign of a systemic issue like chronic inflammation.6 This is not a must have lab parameter, but something to consider if your doctor is comfortable ordering and interpreting this lab.
  • Thyroid Peroxidase (TPO) and Thyroglobulin (TG) antibodies—In addition, I look for thyroid antibodies which can indicate underlying Hashimoto’s disease. Hashimoto’s is sometimes present even with normal thyroid function, and something I screen patients for especially when there is a strong family history.7

The diagram below from the Institute for Functional Medicine is what I use to educate patients during a typical visit with me. It shows how T4 is converted into T3 or Reverse T3, as well as the nutritional and environmental influences that can affect this process.

What are the Ideal Thyroid Lab Values?

As outlined above, there are significant limitations with checking a TSH alone to screen for thyroid dysfunction.8

#1: This starts with the very basic question of what constitutes an agreed upon reference range, which has been debated for years.

The National Academy of Clinical Biochemists states that 95% of people without thyroid dysfunction have TSH of less than 2.5 mIU/L.9

Some investigators have advocated that the upper limit of the TSH reference range be lowered to 2.5 mIU/L, including published work in the Journal of Clinical Endocrinology and Metabolism.10,11.

However the typical reference range used in most U.S. labs has upper limit of normal between 4.5-5 mIU/L, which means that a lot of people may be missing an important diagnosis.

#2: The population-based reference range might not be the same for everyone, and I support a more personalized interpretation of thyroid test results. Don’t get me wrong, I don’t think you should ignore your labs. But perhaps a population-based reference range is different than your ideal reference range as an individual, and some people don’t feel great with a TSH of 4. Of note: fertility specialists typically have tighter guidelines for optimal TSH which is <2.5.12

All that said, my optimal range for thyroid labs is different from a lab’s reference range. I have found clinically (and as a thyroid patient, myself) that the following ranges are where most people feel the best (keep in mind, if you’re on thyroid medications, the timing of your lab draw is important!):

  • TSH 1-2 mIU/L
  • free T4 1.1-1.4 ng/dL
  • free T3 3.2-3.8 pg/mL
  • reverse T3 <12 ng/dL
  • Negative TG and TPO antibodies

The Real Causes of Hashimoto’s (no, your body is not against you)

It can be very unnerving to learn that your immune system is attacking your thyroid (or any other part of your body). Why would your own body betray you like that? It just doesn’t make sense.

Well I’m here to tell you your body is not against you, nor is it unintelligent, or hopelessly broken.

No. There is a reason autoimmune conditions develop.

First off, Hashimoto’s doesn’t “happen” out of nowhere. It is an immune system problem that creates a thyroid issue over time.

Second, there is an underlying cause of autoimmune disease…three causes in fact:

#1: Genetics

#2: Environment

#3: Gut Health

Let’s look at these causal factors individually and in relation to the whole.

Genetics: It’s long been recognized (and proven)13 that genetics play a role in autoimmune conditions, including Hashiomoto’s. However, not every person with a genetic predisposition will develop an autoimmune condition. There’s a saying in epigenetics (the field of medicine that studies genetic expression): “Genes load the gun, environment pulls the trigger.” This explains, to some extent, why two people can have the same genetic predisposition toward a disease, yet only one winds up getting sick.

Environment: Environmental triggers are different for everyone. These may include heavy metals from a dental procedure or certain foods, pesticides from your lawn care service, a food sensitivity to gluten, dairy, or corn which has weakened your gut lining over time, radiation exposure, chronic stress, mold, or many other triggers. Like genetics, environment has been shown to contribute to Hashimoto’s.14

Gut Health: Up until recently, genetics and environment were the main two recognized causes of autoimmunity; but they didn’t really explain the entire picture. Fortunately, pioneering physicians and researchers, like Alessio Fasano, MD, kept asking “why”. About ten years ago Dr. Fasano suggested a third causal factor, intestinal permeability (aka: Leaky Gut).

Dr. Fasano showed that intestinal barrier function15 plays an important role in autoimmunity because it “controls the equilibrium between tolerance and immunity to non-self antigens.” In other words, when intestinal barrier function is compromised, the body’s ability to regulate the immune response is out of balance and autoimmunity ensues.

Specifically, Dr. Fasano identified a protein called zonulin,16 which is released in the presence of small intestinal exposure to bacteria and gluten, among others. Zonulin has been shown to influence the tight junctions in the gut—thus causing an increase in intestinal permeability and autoimmune disease in genetically susceptible individuals.

What does this have to do with Hashimoto’s?

In order to successfully treat Hashimoto’s and see a decrease in antibodies over time, we have to address an individual’s environmental triggers and gut infections—and this will look different for everyone.

Treating Hashimoto’s with Functional Medicine

When you work with a functional medicine physician (like me), we want to understand what’s causing/exacerbating your individual case so we can create a truly custom protocol.

If you’re in the beginning stages, this may mean some simple changes to your diet and lifestyle along with a specific focus on identifying and treating underlying gut infections like small intestine bacterial overgrowth (SIBO), fungal/ candida overgrowth, parasites etc.

If you’re at a more advanced stage, you may benefit from thyroid medication in addition to the above.

With functional medicine, our goal is always to find the root cause of illness, rather than mask symptoms with medications. However most people with hypothyroidism would benefit from prescription medications aimed at carefully and precisely replacing thyroid hormone. In my practice I prescribe both Natural Dessicated Thyroid (like Armour) as well as synthetic medications like Tirosint, Synthroid and Cytomel when appropriate. When prescribed correctly, proper thyroid medications can make a huge improvement in quality of life for many!

The benefit of working with a licensed physician certified in functional medicine is that I can help you manage medications (if necessary) in conjunction with other integrative modalities.

Dietary Solutions for Hashimoto’s: There is no one-size-fits-all when it comes to nutrition, and my favorite way to understand individualized nutrition needs is through nutrigenomics testing. However there are some basic principles to follow:

  • Eliminating trigger foods—this varies for every person, but I consistently recommend eliminating gluten because of the research mentioned above which shows the connection between gluten, zonulin, and autoimmunity.17
  • Cutting back or eliminating refined carbs, refined sugar and artificial sweeteners.
  • Upping your intake of nutrient-dense foods—especially foods high in selenium, zinc, iron, B vitamins and vitamin A.
  • Increasing consumption of healthy fats—such as olive oil, avocado oil, olives, nuts, seeds, and omega-3-fats from wild-caught fish like salmon and sardines.
  • Increasing consumption of gut-healing foods—such as cultured foods (kombucha, kim chi, sauerkraut), bone broths, and prebiotic-rich foods (leeks, onions, green banana, etc.)—this really depends on the individual since some gut infections are best treated before incorporating some of these foods.
  • Eliminating food sources of heavy metals—such as large fish like tuna.
  • Limiting alcohol
  • Limiting iodine-rich foods—most of us don’t get enough iodine in our diet, and under normal circumstances iodine is something I recommend. However, I do not recommend iodine for patients with active Hashimoto’s (high TPO or TG antibodies).

Common Lifestyle Solutions for Hashimoto’s

  • Adopt a low-tox lifestyle—clean water, clean air, clean food. This is a loaded topic and you can learn more by downloading my free ebook 12 Ways To Detox Your Home.
  • Remove heavy metals from your life—these may come in the form of mercury dental amalgams, or other sources. If you have dental amalgams (silver fillings) be sure these are removed safely by an IAOMT certified dentist (otherwise just leave them alone).
  • Reduce stress—stress reduction techniques have been proven18 to benefit autoimmune patients.
  • Practice restorative exercise vs. intense exercise—such as yoga, walking, and Qi gong.
  • Quality sleep—ideally 8-9 hours a night, and maybe more depending on your condition.
  • Meditate—it’s great for stress, sleep, and everything in between.
  • Spend time in nature—getting natural sunlight is great for optimizing immune-boosting Vitamin D, while direct contact with the earth (walking around barefoot or gardening) has been shown to reduce inflammation markers.19
  • If it’s an option, get off birth control pills—again, this is an individualized recommendation, but birth control depletes essential nutrients required for optimal thyroid function, such as zinc and B-vitamins, and increases levels of Thyroid Globulating Hormone, which binds to the very thyroid hormones you need to get healthy.20
  • Professional counseling/therapy—emotions can trigger any type of disease, especially when associated with trauma. If this is a causal factor for you, seeking professional help is not only empowering but it will help you heal much faster.

Supplements that I typically recommend for women with Hashimoto’s disease include:

  • A high-quality multivitamin with Vitamin A, methylated B-vitamins, Iron, Selenium, and Zinc
  • Probiotics, typically MegaSporeBiotic
  • Adaptogenic herbs like Ashwagandha, which has been shown in at least one small study to improve T4 levels21
  • Vitamin D, depending on serum levels

However, due to the individual nature of Hashimoto’s it’s best to consult your doctor about the best supplements for you.

To recap:

  • Hashimoto’s is an autoimmune disease.
  • Over time, it can cause hypothyroidism.
  • Unfortunately, it is not usually diagnosed early because it cannot be detected through basic lab work such as TSH.
  • Hashimoto’s is caused by a combination of genetics, environmental triggers, and gut health; though everyone’s triggers will be different.
  • Functional Medicine has an excellent track-record in helping people diagnose, treat, and overcome Hashimoto’s.
  • Advanced lab work, and other testing is the only way to identify the real cause of and solutions for individual cases.
  • It’s important to educate and advocate for yourself.

Interested in learning more?

As I mentioned earlier, thyroid health issues plagued me for years before functional medicine helped me figure out what was wrong. So, whether you have Hashimoto’s or suspect you may, I’d love to help. Reach out to me and let’s get started on the road back to reclaim your health.

During a functional medicine consultation, we’ll figure out:

  • If your thyroid function is outside of the optimal range
  • And if so — which medication is right for you (i.e. is Synthroid best, or might Armour be a better option?)
  • The root cause of thyroid antibodies and autoimmunity through advanced functional medicine testing like urine organic acids (OAT), DUTCH hormones and adrenals, GI Map stool testing, etc (hint: first we’ll look at the gut, but we won’t ignore your environment)
  • How to address your health concerns through personalized nutrition, lifestyle, and supplement recommendations

Contact my office to learn more!


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  1. https://www.ncbi.nlm.nih.gov/books/NBK459262/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529417/
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529417/
  4. https://www.thyroid.org/hashimotos-thyroiditis/
  5. https://www.thyroid.org/wp-content/uploads/patients/brochures/FunctionTests_brochure.pdf
  6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917573/
  7. https://www.thyroid.org/hashimotos-thyroiditis/
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529417/
  9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957513/
  10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957513/
  11. https://academic.oup.com/jcem/article/98/9/3584/2833082
  12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136077/
  13. https://ghr.nlm.nih.gov/condition/hashimoto-thyroiditis
  14. https://ghr.nlm.nih.gov/condition/hashimoto-thyroiditis
  15. https://www.ncbi.nlm.nih.gov/pubmed/21248165
  16. https://www.ncbi.nlm.nih.gov/pubmed/22731712
  17. https://www.ncbi.nlm.nih.gov/pubmed/22731712
  18. https://www.ncbi.nlm.nih.gov/pubmed/21094920
  19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378297/
  20. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494777/
  21. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296437/

About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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