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In my last article, I showed six different patterns of hypothyroidism that don't show up on standard labs, and aren't sustainably helped by thyroid hormone replacement drugs. The scientific literature has suggested that the leading cause of low thyroid symptoms is an autoimmune condition called Hashimoto's disease. In this article I want to go over some of the underlying factors that need to be looked if you are faced with this autoimmune disease.
Hashimoto's disease, or autoimmune thyroiditis, isn't a new discovery. First mentioned in clinical literature in 1912, it was actually the first disease to be labeled as autoimmune. Your immune system is an intricate, sophisticated network that protects your body against potentially harmful viruses and bacteria. When your immune system mistakes your body as a harmful pathogen and attacks it, this is classified as an autoimmune response.
Hashimoto's can be diagnosed by running thyroid peroxidase antibodies (TPO Ab) and thyroglobulin antibodies (TGB Ab) tests. These tests aren't commonly administered because the treatment would be the same whether you have Hashimoto's or true primary hypothyroidism: thyroid hormone replacement drugs. Because the autoimmune response can go through active and dormant states, there is a chance for a false negative, which is why a comprehensive health history is essential.
Ninety percent of all hypothyroid cases in the United States are autoimmune in nature. Thyroid autoimmune diseases are the most common, affecting 7-8 percent of the population. Whether or not you have primary hypothyroidism, a thyroid hormone conversion dysfunction, or an autoimmune disease, a thyroid hormone replacement drug is the only option given in the mainstream model of care. The problem with Hashimoto's is that the thyroid isn't the actual source of the problem. The thyroid is the victim of the immune system.
Let's go over some of the pieces of the puzzle, the proverbial gasoline barrels on the fire that is the autoimmune thyroid response:
1. Chronic stress
Having chronic emotional or physiological stress can up-regulate or "turn on" an autoimmune reaction. Chronic adrenal stress and elevated cortisol levels can weaken the immune system barriers. Tracking the free-fraction circadian cortisol rhythm and your Adrenal Stress Index will help investigate this important factor.
2. Food intolerances
When someone is predisposed to an autoimmune reaction, commonly ingested foods can cause the already over reactive immune system to act even more erratic. Gluten, grain, milk and soy are some common intolerances that can cause systemic inflammation and exacerbate symptoms. With gluten alone the immune response can last up to 6 months each time you consume a grain containing gluten. A food intolerance panel can be run to gain insight into this.
3. Nutrient deficiencies
Nutrients are essential for overall health and immune function. Vitamin D and selenium deficiencies, among others, have been shown to have a negative effect on the immune system in regards to autoimmune thyroid cases
4. Gut issues
Around 80 percent of your immune system is located in the GI system. When you have a compromised gastrointestinal system such as Leaky Gut Syndrome, chronic infections or Small Intestinal Bacterial Overgrowth, this will have a negative impact on your immune system and your thyroid. Immunological gut labs need to be run to determine if this is a possibility.
5. Toxins
Since World War II, society has been inundated with toxic chemicals. Toxic chemicals and metals can cause an autoimmune response against the thyroid. I run labs such as the urine heavy metals panel to see the patient's toxicity levels.
6. Estrogen imbalances
Imbalances in estrogen levels have been shown to trigger an autoimmune thyroid response in women. Comprehensive estrogen metabolism labs should be done to take this into consideration.
7. Blood sugar dysregulation
Dysglycemia, insulin resistance or conditions like PCOS have been shown to aggravate conditions like Hashimoto's. Having an insulin resistance test run is an essential factor to be looked at
8. Iodine intake
Iodine is the active ingredient in many thyroid supplements on the market, but research has shown excess iodine intake to make problems worse for the Hashimoto's case. Another example of a "one size fits all" approach not being adequate for thyroid care, pharmaceutical and natural approaches alike.
These are just some of the factors that need to be looked at and addressed to fully understand a complex condition and give answers to someone struggling with Hashimoto's disease. You need to deal with all of the underlying factors involved to find a sustainable solution for your optimized health.

Will Cole, IFMCP, DNM, D.C., is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian,The Inflammation Spectrum, and Gut Feelings.
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Learn moreMore from the author:
Functional Nutrition Training
Check out Functional Nutrition Coaching
A cutting-edge nutrition deep dive taught by 20+ top health & wellness experts
Learn more
Will Cole, IFMCP, DNM, D.C., is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian,The Inflammation Spectrum, and Gut Feelings.
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