Getting out of the box to treat Hashimoto’s thyroiditis

 There is a lot that doctors can’t agree on about Hashimoto’s thyroiditis, as I mentioned in my post last week…

That’s why treatments vary so much depending on whether you go to a mainstream doctor who practices purely conventional medicine, versus the functional treatment you might receive from an integrative physician.

What would that functional treatment include? Let’s talk about that…

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How autoimmunity occurs

Remember that Hashiomoto’s thyroiditis is an auto-immune condition where the immune system attacks the thyroid gland. How does auto-immunity occur? The proposed mechanism of action is through three conditions that contribute:

  1. Genetic predisposition: genes can be turned on and off through lifestyle habits. This “epigenetic” effect means that you can carry genes for a particular condition (such as diabetes) and effectively “turn off” these genes from expressing through eating clean, raw foods. This case is demonstrated by the work of Gabriel Cousens, M.D. at his Tree of Life Foundation clinic in Patagonia, AZ where they filmed “Raw for 30 Days.”
  2. Intestinal permeability (a.k.a. “leaky gut”) in which the intestinal lining allows for unwanted proteins to easily enter the blood stream that stimulate the immune system to produce antibodies directed to “self” target tissues; in the case of Hashimoto’s thyroiditis, antibodies are directed to attack thyroid gland tissue.
  3. Unhealthy bacterial population in the wall of the lower small and entire large intestine, which are damaging to the intestinal wall. There are more than 500 bacterial species there, and many of these are unhealthy, competing with the healthy ones known to heal the intestinal lining (such as pro-biotics lactobacilli and bifidobacterial. These healthy bacteria secrete short chain fatty acids that have been proven to heal a damaged intestinal lining.

Dietary recommendations for reversing autoimmunity

Even a healthy food can trigger autoimmunity. A common food is wheat and other grains (spelt, barley, rye, triticale, kamut, farro, durum, bulgar, and semolina. Here are grains that do NOT contain gluten: oats (unless contaminated with other grains in manufacturing), brown and wild rice corn, amaranth, buckwheat, quinoa (“keen-wah”), millet, sorghum, teff, and montina (a.k.a Indian rice grass).

Consider doing a simple targeted “food elimination” experiment. Begin by eliminating gluten (breads, pasta, cereals with wheat flour) for 4 weeks; then reintroduce gluten food products back into your diet for at least 3 days and watch for a recurrence of symptoms. You may have an answer quickly with some symptom involving your skin, joints, pains, sleep, mood, or energy level.  Then, do the same with foods containing dairy, peanuts, soy, eggs, corn, and even with refined sugar foods (the top 7 allergy-causing foods).

A Hashimoto’s expert, Izabella Wentz, PharmD, states that, “While changing your diet is a really important first step that will greatly help many of you (“just the first step”), if you do not see a complete remission of your condition within 3-6 months, I encourage you to dig deeper.” I will dig deeper with you in this article.

Therefore, you will want to consume only whole foods. Remove the top inflammatory foods from your dietary routine such as processed foods, breads, sugars, snack foods and frozen meals high in preservatives and food dyes. Simply notice how many ingredient names that are hard to pronounce, and this will give you an idea of what you should stay away from.

There are many healing foods to consume along with your soups and smoothies, such as cilantro, green tea, turmeric, lemon peel (limonene) and fresh lemon, bone broth, and the fermented foods kombucha, raw fermented sour kraut, and kimchi. The more you eat of fruits, vegetables, seeds, nuts, and legumes in your diet (compared to cooked foods), the better.

You may wonder if this has been proven to work. There are many who write about their story, some smaller studies published in the scientific literature about healing prototype diets for other auto-immune conditions such as Crohn’s disease, but not for Hashimoto’s thyroiditis.

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More methods to help reverse low thyroid function

Here are other strategies for healing Hashimoto’s thyroiditis:

  • Optimize your digestive function: eat slowly; chew food thoroughly; take digestive enzymes; eat probiotic-rich (fermented) foods listed above.
  • Detoxify your liver in the spring and fall of each year: you can take milk thistle and other liver-cleansing herbs. You can often find these as “detox tea” in the local health food store or online.
  • Have enough stomach acid, which is required for optimal nutrient digestion and to protect you from pathogenic infections. Get off any acid-blocking medications slowly while avoiding foods that trigger stomach pains and supplementing with digestive enzyme (a blend) usually works. Betaine HCL is a natural stomach acid supplement but be careful in taking this while getting off acid-blockers such as omeprazole, pantoprazole, and esomeprazole).
  • Get your fasting insulin and leptin levels tested; patients with high reverse T3 levels (the inactive T3 form) almost always have high fasting insulin and high fasting leptin levels. Then you can pursue natural healing for these two conditions.

 Supplements to help reverse low thyroid function

  • Iodine (low to moderate dose; more is not necessarily better)
  • Zinc, selenium, vitamins A, D, E
  • Oil of Oregano has antimicrobial, antioxidant, and intestinal cleansing benefits
  • Tyrosine (an amino acid); you may have enough of this amino acid but it may not be converting the thyroid hormone T4 to the more active hormone T3. Tyrosine supplementation mixes with iodine to help this conversion.
  • Aloe Vera juice from the inner fillet (not from the whole leaf) has been shown to be healing to skin and intestinal lining
  • Slippery elm for digestive health
  • L-Glutamine (higher dose, shorter duration, then repeat) for optimal digestion
  • Probiotic Saccharomyces boulardii (a strain of baker’s yeast) for example, is a yeast that has been proven by clinical trials to prevent and treat several gastrointestinal diseases through multiple mechanisms of action.
  • Probiotics are otherwise healthy bacteria. Look for a blend from a trusted source with more than 20 billion colony-forming units (cfu) per capsule of “live” or “active” bacterial strains. One particular strain may make you feel worse. A blend of saccharomyces boulardii, lactobacilli and bifidobacterial may be the best.
  • Glutathione is one of the master anti-oxidants and energy-producing molecules in our bodies. Your glutathione becomes depleted through aging, infections, pollution, poor diet, toxins, medications, stress, trauma, and radiation. Taking glutathione as a pill is not effective because your stomach acid and pancreatic enzymes will digest this protein. Therefore, glutathione-boosting supplements needed to produce and recycle glutathione include milk thistle (silymarin), 5 methyl-tetrahydrofolate, alpha-lipoic acid, and N-acetyl-cysteine.
  • Proteolytic enzymes (different than digestive enzymes) digest the protective protein coating of pathogens (such as bacteria, viruses, parasites, fungi and candida). This effectively weakens and kills them. They are thought to safely and effectively clean the bloodstream. Systemic enzymes have been quite extensively studied in Germany by the company that manufactures Wobenzym® N, and Wobenzym® There are many companies now manufacturing them from animals (trypsin, chymotrypsin), plants (bromelain, papain), bacteria (serrapeptidase), or fungi (Serrazimes®).  The peer-reviewed scientific literature is replete with more studies at

There’s more to learn about this approach to healing low thyroid function such as low dose naltrexone (LDN), which I’ll save for a later article.

To healing and feeling good,

Michael Cutler, M.D.


  1. As described by Dr. Alessio Fasano, a world-renowned gastroenterologist, Celiac disease expert and researcher in gut autoimmunity.
  2. Konijeti GG, Kim N, Lewis JD, Groven S, Chandrasekaran A, Grandhe S, Diamant C, Singh E, Oliveira G, Wang X, Molparia B, Torkamani A. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 Nov;23(11):2054-2060. PubMed PMID: 28858071.
  3. Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therap Adv Gastroenterol. 2012 Mar;5(2):111-25. PubMed PMID: 22423260.
  4. Biziulevicius GA. Where do the immunostimulatory effects of oral proteolytic enzymes (‘systemic enzyme therapy’) come from? Microbial proteolysis as a possible starting point. Med Hypotheses. 2006;67(6):1386-8.
  5.  Jager H.: Hydrolytic Enzymes in the therapy of HIV disease. Zeitschr. Allgemeinmed., 19 (1990), 160.
  6.  Bartsch W.: The treatment of herpes zoster using proteolytic enzymes. Der Informierte Arzt. 2 (1974), 424-429.
Dr. Michael Cutler

By Dr. Michael Cutler

Dr. Michael Cutler is a graduate of Tulane University School of Medicine and is a board-certified family physician with more than 20 years of experience. He serves as a medical liaison to alternative and traditional practicing physicians. His practice focuses on an integrative solution to health problems. Dr. Cutler is a sought-after speaker and lecturer on experiencing optimum health through natural medicines and founder of the original Easy Health Options™ newsletter — an advisory on natural healing therapies and nutrients. His current practice is San Diego Integrative Medicine, near San Diego, California.