Hashimoto’s Part 3: Treatment Approaches

Make a connectionWith Hashimoto’s and other autoimmune conditions, it’s not a case of one day you don’t have it and the next day you do. 

It takes time to develop, and we know that antibodies can be found up to 7 years before diagnosis!  Halting the process of autoimmunity takes time, and is possible.  That is one of the reasons I love the functional medicine model! 

Full spectrum functional medicine involves evaluating and treating potential imbalances in biology and health.  This is done via mapping out information in what the Institute for Functional Medicine calls the “Matrix”, which serves as a visual guide and roadmap for care.  I utilize the Matrix in combination with Dr. Datis Kharrazian’s methods, which includes the following categories and corresponding questions to consider:

  • Lifestyle: Are foundational elements that support immunity and biology optimized?  This includes sleep/relaxation, exercise/movement, nutrition, stress, relationships, and mindset/emotional factors.
  • Nuances of nutrition: Even if someone eats “perfect”, blood sugar imbalances, inflammatory elements in natural foods (e.g. lectins, oxalates), and even salt may be playing a role in triggering autoimmunity.
  • Assimilation: Is someone able to absorb and use nutrients/oxygen via the gut and lungs? 
  • Defense and Repair: Is the immune system dealing with inflammation an subacute infections (e.g. Epstein-Barr virus, H. Pylori bacteria), affecting its ability to work effectively?  If present, these may be driving a process known as molecular mimicry or bystander activation.
  • Energy: Does the body have the support and nutrients/antioxidants needed to make sure the mitochondria are working well? Many patients with Hashimoto’s have fatigue, and mitochondria play a significant role in this.
  • Biotransformation and elimination: Is the liver, gut, kidneys, and skin properly working to clear out “waste” from our body (waste can be from normal biological functions, environmental exposures, etc)?
  • Transport: Can oxygen and immune cells be delivered effectively to target tissues (via lymphatic system, cardiovascular system)?
  • Communication: Are hormones and neurotransmitters in balance?  This includes insulin, cortisol, estrogen, thyroid hormones, and more.
  • Structural integrity/Barriers: Are barriers and cell membranes supported and robust, so that the cells can actually make and use thyroid hormones appropriately?  We have barriers that protect us throughout our body (e.g. intestinal, blood-brain barrier, lungs, nose/mouth), but these become compromised and trigger an immune response. 

I want to note that we don’t have to optimize each of the above (with the exception of lifestyle).  The body is smart, and when you start to remove barriers to balance, other elements that are out of balance will improve.  Evaluating the above is part of my process, but for anyone interested in mapping out the “Matrix” for themselves, I recommend my colleague Dr. Lara Salyer’s online workshop (cost is $40).

To truly address treatment would require a book’s worth of content! But my goal is to guide patients on self-care and empowerment, with or without seeing me, so the following information will serve as a basic guide.  It is not medical advice, simply education.  As with any content you find free on the internet, it is always important to discuss risks and benefits of anything in which you choose to partake with a knowledgeable licensed healthcare practitioner. 



By the time someone has symptoms caused by Hashimoto’s, up to half of the thyroid can be destroyed, so many people require prescription thyroid medication to compensate for this loss.  Around 2/3 of patients will feel better (not just have normal looking labs) just by taking the commonly prescribed Synthroid (“T4”).  But for the 1 out of 3 patients who don’t feel better, the other options are often needed. 

Thyroid hormone replacement medications include:

  1. Levothyroxine (“T4”) (e.g. Synthroid, Tirosint)
  2. Liothyronine (“T3”) (e.g. Cytomel)
  3. Combination of T3 + T4 (made via a compounding pharmacy)
  4. Natural desiccated thyroid gland (“NDT”) (sourced from animal thyroid glands, and includes T3 and T4, in addition to thyroid hormones that have no known direct function – T1 and T2).  Of note, I have seen NDT worsen autoimmunity in a few patients, i.e. raise antibodies, so monitor labs accordingly if your primary care provider prescribes this.

Both mainstream medical practitioners and functional medicine providers who are physicians, NPs, or PAs can prescribe the above.

The most common mistake I see, with both patients and practitioners, is a myopic focus on using thyroid hormones to make labs look perfect.  The goal is not perfect labs – the goal is to feel better.  And if the thyroid hormones are not doing that, that is an indication to look beyond the thyroid.



Lifestyle habits are the foundation of creating or destroying health.  It is the most simple in concept, most difficult to change, and the most overlooked factor in all medical models (even functional medicine!).

Mainstream medicine notes the importance of lifestyle, but doesn’t know how to address it beyond “eat less and exercise more”.  It’s much faster and easier to prescribe a pill rather than use education and time to discuss ways to modify daily habits.  I was educated in this model, and I don’t fault my colleagues (or patients) for their lack of knowledge in this area.  I also don’t place judgement on those who want a quick fix (it’s human nature!).

I like to look at lifestyle habits as influencing 2 key requirements for life: nutrients and oxygen.  These drive biological imbalances including thyroid hormone imbalances, and are affected by the food we eat, our sleep quality, the physiological effects of stress (e.g. shallow breathing decreases oxygen), and more.

Here is a basic overview of lifestyle elements:

  • Food/Nutrition: Food provides the building blocks of biology!  We must eat to survive, and we need nutrients to thrive.  When people with autoimmune conditions first start making changes in dietary choices, I recommend following the Whole30 or Autoimmune Paleo Protocol for 6-12 weeks.  There are many resources and recipes for these online, and both of these focus on eliminating inflammatory foods and eating more nutrient-dense foods.   
  • Nutrients: The building blocks of thyroid hormone production include nutrients in every step.  I call these part of the “recipe” for making hormones – and they are needed in the right proportion. Some of these include selenium, vitamin D, zinc/copper, vitamin A (retinol form, not the form found in vegetables), B vitamins, and iodine.
  • Sleep: Our thyroid hormones are produced in highest quantities between midnight and 2am, and fluctuate over the course of the day. Things to consider:
    • Are you getting deep sleep and enough of it?   
    • Are you being exposed to blue light while sleeping or an hour before (e.g. from screens)?  Blue light affects melatonin production, so make sure your room has no light (even from a clock)
    • Do you have pets or seasonal allergies?  Consider use of an air purifier in your room.
  • Movement/Exercise: Moving our body increases oxygen uptake in our muscles and cells.  But we need this in a balanced amount.  It is not uncommon for me to see patients who exercise too much or too hard (which causes stress on the body).
  • Relationships: We are highly influenced by the people with whom we spend the most time.  If they are not supportive, encourage unhealthy behaviors, or increase stress, it is important for patients with autoimmunity to decrease exposure to these individuals.
  • Stress:  Our physical response to stress affects how our body uses and makes thyroid hormones (think of stress as running from a threat – the body will direct its energy on running rather than on metabolism, i.e. thyroid hormones).  Stress is not a thing, but a response.  We will never eliminate stress, but we can impact how we react to it.  Here are some tips:
    • Do you get outside for 30-60 minutes per day?  Exposure to UV light and the outdoors has a lot of benefits in our calming the body and supporting immunity.
    • Do you do something everyday that is relaxing?  Watching TV does not count (this is actually a stimulating activity).
    • Are there small things you can do to control your “stress level”?  For example, getting up earlier to take time to enjoy your coffee/breakfast, writing out a to-do list, avoiding email or social media for at least an hour before bed.
    • Consider your personality – are you “addicted” to stress?  This is common in those with “type A” and perfectionist-type personalities.
    • Limit extracurricular screen time (especially social media) to 1-2 hours per day.
    • Meditate – even Harvard backs up the importance of this when it comes to immunity, sleep, mood, and more!



We cannot live in a pristine environment, but we can control various aspects of our environmental exposures.  When it comes to optimizing your environment, I recommend the following:

  • Drink and shower in clean filtered water (refrigerator filters aren’t great at doing this, unfortunately).  The upfront costs for these can seem expensive, but over time, they will save money and improve health.  I typically recommend Berkey water filters for drinking/cooking (filters lasts 5 years, with proper maintenance) or reverse osmosis systems.  And a basic $30 shower filter will last up to 6 months.
  • Decrease exposure to topical and inhaled chemicals by swapping out products that can cause health problems.  Anything that comes in a bottle can impact health, including makeup, shampoo, cleaning products, and more.  I recommend searching for the products you currently use in the Environmental Working Group’s database to see how they rate (aim for 90% of your products to be in the “green” rating).  Pay close attention to anything that you put on your skin and leave on your skin (our skin absorbs up to 70% of what we put on it).
  • Eat more organic foods, by focusing on avoiding the “Dirty Dozen, at home and when at restaurants (for example, kale and strawberry are on this list – try to only consume these when they are organically grown).
  • Consider use of a high quality air filter in the areas where you spend the most time (bedroom and desks are the most common locations).

All the above can seem over-the-top, but I’d rather someone spend money on these instead of expensive functional medical tests.



As noted in the beginning, a properly trained functional medicine provider will evaluate potential biological and health imbalances via a systems-based approach. 

More than half of these are addressed via the first few steps I outlined above.  When more guidance is needed, including labs and personalized supplement recommendations, this is where functional medicine can excel.

In a functional medicine evaluation, a lot of time is spent on collecting information about a patient’s health journey and habits.  Testing choices is often guided by this information, and can help prioritize next best steps. 

No test is perfect, and we have to be careful to avoid over-reliance on test results (or trying to make a test look perfect).  My go-to test is a basic blood test, which is often able to be billed to insurance.  When we need to dive deeper, additional testing options include:

  • Stool tests (looks for how well someone is digesting food, presence of good/bad “bugs”, inflammation)
  • Organic acids testing (urine-based test that looks for metabolites of energy production and detoxification; results often treated with high dose supplements)
  • Food sensitivity testing (blood-based test, not one that I use often especially in the first few months of working with someone; the ones I find most valid are very expensive but can be life-changing)
  • Hormone metabolite testing (salivary or urine-based, e.g. DUTCH testing)

Combining a patient’s personal habits, preferences, health history, and test results guide the treatment process.  The following are part of my approach and “tool kit” of treatments:

  • Prep +/- biofilm disruptors: This may include avoiding certain foods, or using a “medical food” temporarily. 
  • Therapeutic and personalized protocol: These typically last 2-12 months, depending on the severity of symptoms and response.  Food, supplements, herbal remedies, working on mindset with a counselor or self-directed program, and pharmaceuticals are usually needed.  On average, when a patient follows through with appointments and maintains communication with me, a protocol can be completed in less than 6 months (this typically includes 3-5 visits with me).
  • Transition to maintenance and resiliency: When someone has at least 80% improvement in symptoms, and autoimmunity appears to be in remission, the long-term goals need to focus on a few key supplements, identifying triggers, and how to handle flare-ups (which will happen!).

Admittedly, there is a reliance on pills (pharmaceutical or nutraceutical) in the functional medicine model.  Contrary to popular opinion, functional medicine is not intended to switch out “natural” pills for pharmaceuticals (aka “green allopathy”).  I believe we often place too much power in these and have to be careful not to over-rely on them.  For this reason, I don’t tend to recommend as many supplements as my colleagues, and I find it is often beneficial to refer patients to practitioners that are experts in other treatment modalities!

Ultimately, the goal of functional medicine is not to identify and eliminate every specific cause or trigger, but to re-establish normal immune function.  Our bodies are smart, but they sometimes needs to be re-directed! 

The information contained in this article is for educational purposes only.  It does not constitute a diagnosis or prescription for treatment.


  • Hashimoto’s is caused by the “perfect storm” of genetics + environmental triggers + gut hyper-permeability.
  • A lot can be done without requiring expensive tests and supplements – always start with the first 3 steps, and use a health coach or nutritionist if needed!
  • Pills have a purpose, but these can carry risks as well.  We really don’t know the effects of combining a lot of supplements (and these may actually be antagonistic rather than synergistic).  Single ingredient and less supplements often work better in those with Hashimoto’s.
  • Advanced lab work and interpretation by an educated healthcare practitioner is the best way to evaluate for individual triggers and causes behind autoimmunity.
  • Do not try to make test results “perfect” – focus on feeling better. And if you still have symptoms, consider other contributing factors beyond changing thyroid medication doses or chasing thyroid lab results. 

If you need guidance, I’d love to help!  Starting in January 2021, I’m joining the amazing team at Parsley Health – learn more about this 100% virtual practice here!

Thank you for taking the time to read – I hope I provided some useful information and guidance for you!