Holistic Healing Protocol For Hashimoto's


Hashimoto’s is an autoimmune disease of the thyroid.  In general, autoimmune disorders involve the immune system producing antibodies - proteins that are meant to stop intruders (such as viruses and parasites) from harming the body - that end up attacking the body’s healthy tissue. In Hashimoto’s, the body identifies thyroid hormone as a foreign invader, so it produces antibodies and attacks the thyroid; causing inflammation and destruction of the gland over time. Naturally, this negatively impacts the functioning of the thyroid gland. Hashimoto’s is believed to be the most common cause of underactive thyroid or hypothyroidism. The disorder is not a problem of the thyroid gland itself - rather, it’s a condition that stems from overreactions of the entire immune system.


Initially, symptoms may not be present.  As the attack progresses, the damaged cells of your thyroid become inefficient at converting iodine to thyroid hormones.  Your thyroid compensates by becoming larger (also called a goiter) - you may have a sore throat, or you may feel a tightness when you swallow.  Eventually, the symptoms of hypothyroidism will be felt (see Guide to Supporting the Thyroid for specific symptoms) caused by the lessening function of your thyroid due to the destruction.  You may then oscillate between these hypo symptoms one day, and hyper symptoms the next.  Hyperthyroid symptoms include anxiety, a racing heart and palpitations - all of which are caused by the release of thyroid hormones into your blood due to the destruction.  


If you suspect you may be suffering from Hashimoto’s, you can request that your doctor run two simple labs for thyroid antibodies: thyroglobulin (TG) and thyroid peroxidase (TPO).  The presence of these antibodies will confirm Hashimoto’s.


The hypothalamus, also referred to as the brain’s control center, is responsible for stimulating the production of the two primary thyroid hormones, T3 and T4, when it senses a need for more. It sends a message to the pituitary gland, also known as the master gland, to release thyroid stimulating hormone (TSH) which tells the thyroid to produce T3 and T4.  This process does not occur in people suffering from Hashimoto’s. This can be due to insufficient T4 conversion to T3, the hypothalamus incorrectly communicating with the pituitary gland, or the pituitary gland not responding to signals to release TSH.


The roles of the thyroid gland are all impacted in either a hyper- or hypothyroid state. Changes in metabolism, heart function, digestion, energy levels, appetite, sleep ability, mood, and the growth of hair, skin, and nails can all occur.



Fortunately, most of the causes and risk factors that can lead to the development of Hashimoto's can be controlled and prevented through diet and lifestyle alterations. The most important aspect of reversing Hashimoto’s is to identify the root cause of why you, specifically, have developed the condition and to then focus on treating that aspect.


Common causes include leaky gut syndrome, disordered digestive function, candida, consuming inflammatory foods, consuming foods that one is allergic/sensitive/intolerant to, emotional stress, and nutrient deficiencies. Risk factors include being a woman, being middle-aged, having a family history of autoimmune conditions, experiencing a trauma, living with consistently high levels of stress, smoking cigarettes, and having a history of an eating disorder or exercise addiction.  Pregnancy can be a strong precursor to developing Hashimoto’s since the increased activity of the immune system can either worsen an autoimmune disease you already have (such as thyroiditis) or cause it to appear. Menopause may also be a similar trigger.


If you have one autoimmune disease (such as Hashimoto’s), this unfortunately puts you at risk for developing other autoimmune diseases; specifically, celiac disease, Pernicious Anemia (vitamin B12 deficiency) and autoimmune attacks on your adrenals.  Type 1 diabetes can also go hand-in-hand with Hashimoto’s in susceptible individuals. Therefore, prevention and proper management through diet and lifestyle is critical to not only healing Hashimoto’s, but avoiding an additional autoimmune burden.



Eighty percent of our immune systems exist in our guts (i.e. our small and large intestines). When the gut is compromised by increased permeability (leaky gut), the immune system is also compromised. In leaky gut syndrome, holes in the intestinal lining can develop and grow, allowing undigested food particles to pass through and into the bloodstream. When large particles enter the system, the body identifies them as foreign and begins attacking them and anything that has a similar molecular structure. If the food protein has a similar structure to a protein that makes up an organ, then the body can mistakenly begin to attack itself. In the case of Hashimoto’s, the gut becomes leaky due to diet and lifestyle choices, which allows large particles of food, including gluten, to leave the gut and travel to the bloodstream. Gluten has a very similar structure to the proteins that make up the thyroid gland. This results in the body attacking the gluten as well as the thyroid. Any person with Hashimoto's is advised to adopt an anti-inflammatory and gluten-free diet to alleviate symptoms and to increase thyroid functioning.  The focus of a Hashimoto’s diet is on removing inflammatory foods, replacing them with nutrient-dense foods, reinoculating the gut with good bacteria to promote healing of the gut, and consuming foods that are healing for the small and large intestine.


Consume Gut-Healing Foods


Probiotic foods: These included fermented foods such as kefir, kimchi, kombucha, natto, sauerkraut, and other fermented vegetables. Probiotics - essentially good bacteria - are necessary for inoculating the gut with beneficial bacteria, balancing the microflora, and allowing the gut to heal. This can reduce leaky gut syndrome, increase nutrient absorption, and decrease inflammation and autoimmune reactions.


Bone broth: The contents of organic bone broth, such as L-proline, L-glycine, L-glutamine and collagen, can help repair the digestive lining and improve symptoms of hypothyroidism. Bone broth also contains minerals the average person is deficient in, including calcium, magnesium, phosphorus, and silicon. This means that drinking bone broth will simultaneously help repair leaky gut and enhance digestion while providing essential nutrients. Beef and chicken bone broth can help to eliminate food sensitivities, improve energy levels, fight fatigue, increase immunity, and decrease muscle and joint pain.


Fruits and vegetables: These nutrient-dense foods should make up the majority of a Hashimoto’s healing diet. They’re high in a multitude of vitamins, minerals, and antioxidants. The greater variety of foods consumed, the greater variety of nutrients will be consumed. Both vegetables and fruits improve overall digestive health, brain function, heart health, and hormone balance, and help to support a healthy weight. Make sure to buy organic and focus on “eating the rainbow” to ensure that all-important variety.


Wild-caught fish: The most valuable nutrients that wild-caught fish provides are omega-3 fatty acids (EPA and DHA). Omega-3s are essential for hormonal balance and thyroid function. Balancing omega-3 fatty acid foods to omega-6 fatty acid foods in a 1:3 ratio is ideal for reducing inflammation, supporting healthy neurological function, enhancing mood, and increasing neurotransmitter activity. The best sources of fish are small cold-water fish, such as Atlantic mackerel, Alaskan salmon, and Pacific sardines.


Coconut oil: This oil is a staple in the hypothyroidism-healing diet because it has a high smoke point, is easy to digest, nourishes the digestive system, and has antimicrobial, antioxidant, and antibacterial properties that work together to reduce inflammation. Coconut oil also contains medium-chain fatty acids, which support metabolism function, increase energy levels and brain function, and stabilize blood sugar levels.


Seaweed: Good sources of seaweed, including kelp, nori, kombu, and wakame, are the most potent sources of iodine. Iodine is the central element in thyroid hormone, so it plays a very important role in overall thyroid functioning.


Sprouted seeds: Alpha lipoic acid (ALA), which is found in flax, hemp, and chia seeds, is a type of omega-3 fatty acid that assists with proper hormonal balance and overall thyroid function. In general, high amounts of good fats support healthy brain functioning, improve mood, and lower inflammation. Sprouting the seeds - essentially germinating them before consumption - reduces the levels of anti-nutritional compounds found in raw seeds, making them more nutritious and easier on the digestive system.


Filtered water: Water is incredibly important for the proper functioning of all body systems. It hydrates the body, enhances digestive function, prevents fatigue, enhances mood, eliminates constipation, and reduces sugar cravings. Aim to drink 8 to 10 glasses of water consistently throughout the day, or calculate the amount that you need optimally by dividing your weight (in pounds) in half - now drink that many ounces daily.


High-fiber foods: It’s common for people with Hashimoto’s to have digestive issues. Fiber is essential for balancing blood sugar levels and improving digestive health as well as heart health. Fiber also helps you feel fuller for longer, which can help lower and stabilize weight. High-fiber foods include fruits and vegetables, legumes, coconut, nuts, and seeds.


Selenium-rich foods: Selenium is required for the production of the T3 thyroid hormone. Ensuring adequate levels of selenium in the body can reduce autoimmune effects, especially in Hashimoto’s, because the thyroid has the highest selenium content in the body. Selenium specifically helps thyroid function by improving the overall structure of the thyroid gland and decreasing the antibodies that are targeting thyroid proteins. Excellent sources of selenium-rich foods are Brazil nuts (maximum 4/day), sunflower seeds, sardines, grass-fed beef, and organic chicken.


Avoid Inflammatory Foods


IgG and IgE tests will help you to determine which foods you’re sensitive to and allergic to, respectively. These tests are recommended because food sensitivities are incredibly common these days, and eating foods your body is sensitive to will continuously promote inflammation, which will prevent healing from taking place. The following groups of foods are some of the most common sensitivities and hormone disruptors:


Gluten: As mentioned previously, gluten is a protein with a very similar molecular structure to the proteins that make up the thyroid gland. When gluten enters the bloodstream, those sensitive to it will elicit an immune response which produces inflammation. Many people with thyroid issues are sensitive to gluten. Gluten is found in all wheat, rye, and barley products, as well as in many other products such as alcohol, soy sauce, and packaged foods. If avoiding gluten, it is therefore essential to read labels closely.


Conventional dairy: The issue with conventional dairy is that it has been pasteurized and homogenized. Pasteurization - the process of heating the milk at high temperatures to kill pathogens - damages and denatures the proteins, enzymes, nutrients, and other components found in raw milk, making it hard to digest which can trigger reactions that raise an inflammatory response. Homogenization - the process of mechanically breaking up the large fat globules found in milk into smaller globules, so that the milk will mix together evenly for a desirable consistency without separating - also has inflammatory results, as the resulting fat globules become unnaturally reassembled and combined with proteins, making them hard to digest.


Sugar: One of the thyroid’s primary functions is hormonal balance and metabolism regulation. When consumed, sugar can disrupt the hormonal balance necessary for proper metabolism functioning. Sugar should therefore be avoided entirely, as it can contribute to hormonal disturbances, fatigue, mood changes, worsened depression, and weight gain. If you’re suffering from Hashimoto’s, avoid sugar in all of its forms, including honey, agave syrup, and maple syrup. High-sugar fruits (such as bananas, mangoes, dates, and watermelon) should be eaten rarely and in moderation.


Refined flour products: These products can also negatively impact hormone levels and contribute to weight gain. Refined flour products include bread, cereals, pasta, and all baked goods. These products should be replaced with quinoa and buckwheat-based goods or with baked goods made with coconut flour or almond flour.


Goitrogens: These include raw cruciferous vegetables such as broccoli, cauliflower, cabbage, kale, soy, and Brussels sprouts. Goitrogens are molecules which impair thyroid peroxidase, an enzyme required for thyroid hormone production. If consuming cruciferous vegetables, it’s best to steam them for 30 minutes (rather than eating them raw) and to keep portion sizes moderate.


Tap water: This water source is typically contaminated with fluoride, an endocrine disruptor, and chlorine, an inhibitor of iodine absorption.



Iodine use in Hashimoto’s is a bit controversial, but nonetheless, critical for proper thyroid functioning and thyroid hormone synthesis.  The key is NOT to take it in isolation, but with supporting nutrients which also assist in toxin detoxification caused by iodine use.  They include, most prominently, selenium (200-400mg/day), vitamin C (2000-5000mg/day), unrefined sea salt (1/2 tsp per day), magnesium (400mg) and B-vitamins, with an emphasis on B2 and B3.  A few of these will be discussed in more detail below. It is best to start small with iodine (Dr. David Brownstein, the world’s foremost expert on iodine, recommends a minimum of 12mg) and increase/decrease depending on your symptoms.  You may find that you’ll need more one day, and less the next, depending on whether you’re experiencing hyper- or hypo-thyroid symptoms.


Probiotics: As mentioned earlier, healing Hashimoto’s requires healing the gut and reducing inflammation. Probiotics support gut health and reduce inflammation by balancing microflora in the small and large intestine and help to repair the digestive lining which reduces food sensitivities and improves immunity.  A good probiotic will contain multiple residential strains such as L-acidophilus and Bifido Bacterium. A capsule containing 25-50 CFU (colony forming units) of live cultures per day is advised.


Vitamin D: Vitamin D is a common deficiency in people with Hashimoto’s and in fact, puts you at risk for developing the disease. The benefits of sufficient vitamin D levels include regulation of the immune system and hormonal balance. Laying in the sun with plenty of skin exposed (and no SPF) for 15-30 minutes between the hours of 11 am and 3 pm is enough to get your daily vitamin D dose, but this is not possible for everyone. Supplementation of vitamin D3, in doses of 2,000-5,000 IU/day will provide the same effect.


B-complex vitamins: All of the B vitamins provide a slew of benefits. Vitamin B12 is especially beneficial for healing Hashimoto’s, as it dramatically improves energy levels and healthy cellular functioning.  It is also important to emphasize vitamin B2 and B3 for their use in energy metabolism. 1-2 capsules daily of a complete B-complex, taken at breakfast and lunch. Avoid taking B vitamins in the evening as they may have the effect of interfering with sleep.  Also, 100mg of vitamin B2 and 500mg of vitamin B2 twice per day will help stimulate ATP production (energy metabolism).


Selenium: As discussed, selenium is required by the thyroid gland to manufacture and regulate T3 and T4.  It can also help lower the high levels of antibodies, especially TPO. Supplementation will ensure that any deficiency is counteracted, on top of a diet rich in foods containing selenium.  200-400mcg/day is recommended (do not exceed 400mcg total between supplementation and food).



Ashwagandha: This adaptogenic herb helps to reduce thyroid issues by enhancing the body’s ability to respond to and handle stress and balancing hormones. The hormones it benefits include T4, which assists with overall healing of Hashimoto’s.  Try 5mL of tincture 3x/day.


Turmeric: The active component in turmeric, curcumin, reduces inflammation and pain. The best way to use turmeric is in homemade teas, lattes, and elixirs, or to sprinkle it on your favorite dishes.  When there are elevated TPO antibodies, it is important to remove inflammation in the system. Try 1,200-2,400mg per day of concentrated curcumin.


Reishi: The antioxidants and anti-inflammatory compounds in reishi mushrooms improve nerve transmission to the brain, enhance endocrine system functioning, and help to balance hormones naturally. Reishi also lowers the number of toxins and heavy metals accumulated in the body, which improves energy levels, concentration memory, and sleep.  Try 5mL of tincture 3x/day.


Guggul: in herbal medicine, Guggul has been shown to improve thyroid function, increasing conversion of the inactive T4 hormone to its active T3 form.  DO NOT use during pregnancy, but safe to use while breastfeeding. Try 750mg per day.



Environmental factors play a role in Hashimoto’s, as do lifestyle factors such as stress. Follow these tips for healing and preventing the disorder:


Throw out chemical-based products and replace them with natural products: Consider the ingredient lists of your cosmetics, body wash, shampoo, conditioner, moisturizer, deodorant, household cleaning products, laundry detergent, and anything else found in your home. The chemicals found in conventional products can be endocrine disruptors, and the thyroid is a vital endocrine organ. Using these products can worsen Hashimoto’s symptoms. Replace them with natural and/or homemade products. There are many natural cosmetic and personal care products now widely available on the market. Cleaning products can be easily made at home using white vinegar, lemon, and essential oils like peppermint, lavender, and frankincense. Moisturizers can be replaced with all-natural oils that contain healing benefits.


Avoid plastic and aluminum: Plastic contains estrogen-mimickers that can disrupt the body’s entire hormonal balance. Aluminum is a toxic metal that is a neurotoxin and a potent immune stimulator which impairs immune functioning. Aluminum can be found in cookware, tinfoil, deodorants, and cosmetics.


Manage stress: People with autoimmune symptoms often experience extreme emotional stress before the onset of the disease. Stress triggers alterations in the production of neuroendocrine hormones and contributes to immune dysregulation. It’s essential to choose stress-reducing techniques that work for you and that you enjoy. The techniques you choose can include meditation, reading, exercising (yoga, barre, Pilates, hiking, and resistance training are some great options), journaling, taking Epsom salt baths, spending time outdoors, and spending time with friends and family.


Assess birth control options: Birth control pills and other hormonal forms of birth control such as patches and IUDs prevent pregnancy by using synthetic hormones. These synthetic sex hormones can have a negative impact on other hormones, including thyroid. Additionally, they disrupt the microflora balance in the gut, which can contribute to leaky gut syndrome.


Remove amalgams and silver fillings: These heavy metals disturb hormonal balance and can be removed by a DAMS-certified dentist.



If you haven’t been diagnosed with Hashimoto’s but suspect low thyroid functioning, prevention is key. Follow these tips to maintain hormonal balance and healthy thyroid function:


Ensure adequate levels of selenium and iodine in the body: These are the trace minerals crucial for thyroid function as they produce and are a component of thyroid hormone. A deficiency increases the risk of developing thyroid disorders, including Hashimoto’s. A selenium deficiency also inhibits the activity of glutathione, a potent antioxidant that controls inflammation.


Reduce the risk of developing leaky gut syndrome: An unhealthy ratio of good to bad bacteria can contribute to nutrient deficiencies and raise autoimmune activity in the body. Food sensitivities or allergies, including those to gluten and dairy, can trigger gut inflammation. Other causes of a damaged gut are high stress levels, toxin overload from diet and the environment, and bacterial imbalances. To reduce risk, take a daily probiotic or eat probiotic-rich foods daily and eliminate common food sensitivities.


Manage emotional stress: Stress negatively impacts hormonal balance and is known to worsen inflammation. Stress raises levels of cortisol and adrenaline, which disturbs neurotransmitter function and aggravates symptoms of thyroid disease. These symptoms include low energy levels, poor mood, low concentration, disturbed appetite, weight gain, and the inability to get restful sleep.


Stay active: Exercise is essential for controlling chronic stress and managing hormone-related neurological function. Regular exercise reduces major risk factors and symptoms of Hashimoto’s: it enhances sleep, increases energy, and helps in maintaining a healthy weight.


Whether you’re healing and reversing Hashimoto’s or trying to prevent it, a holistic approach that includes diet and nutrition as well as lifestyle alterations is essential. All the various components of our bodies and minds are intricately connected, so supporting overall health with a focus on thyroid health is the key to healing and preventing Hashimoto’s.