Basics of immune balancing for Hashimoto’s

August 30, 2010 in Thyroid Disorders | 16 comments

balanceIn the first post in this series, we established that hypothyroidism is caused by an autoimmune disease (called Hashimoto’s) in the vast majority of cases. Since then, we’ve explored the role of gluten intolerance, vitamin D deficiency, supplemental iodine, blood sugar imbalances, adrenal stress and a leaky gut in perpetuating the autoimmune attack and disrupting thyroid function. We’ve discussed why dietary changes are always the first step in treating Hashimoto’s, and why replacement thyroid hormone is often necessary for a successful outcome.

What we haven’t discussed yet, however, are specific strategies for bringing the immune system back into balance. That will be the focus of this article.

Originally, I planned to go into considerable detail on the specific mechanisms of immune dysfunction that occur with Hashimoto’s, including a review of immunology, immune system classification (i.e. Th1 or “cell-mediated” immunity vs. Th2 or “humoral immunity”) and immune cell organization. It quickly became clear that such an approach would require an entire series of its own.

So, as fascinating as all of that stuff is, I decided to cut to the chase and focus on the practical, clinical applications. But there’s a caveat. Although I’ll be offering some general guidelines here for how to balance the immune system, if you have Hashimoto’s (or any other autoimmune condition) it’s in your best interest to find someone who understands immunology and is current with the latest nutritional and botanical protocols for treating autoimmune disease.

Why? Because autoimmune disease is not only extremely complex, but also highly individualized. Hashimoto’s in one person is not the same as Hashimoto’s in the next person. In one person, Hashimoto’s could present as a Th1-dominant condition. In another, it may present as Th2 dominant. In still another, both the Th1 and Th2 systems might be overactive, or underactive. And each of these cases requires a different approach. For example, botanicals like echinacea and astragalus stimulate the Th1 system. If someone with Th1 dominant Hashimoto’s takes these herbs, they’ll quite possibly get worse. On the other hand, antioxidants like green tea and Gotu Kola stimulate the Th2 system, and would be inappropriate for those with Th2 dominant Hashimoto’s. (For more information on the specifics of Hashimoto’s autoimmune physiology, see this article on Dr. Kharrazian’s blog and pick up a copy of his book.)

The good news, though, is that there are general approaches to balancing the immune system that are suitable for all types of Hashimoto’s regardless of the specific pattern of immune dysregulation. These approaches can be broken into three categories: removing autoimmune triggers, enhancing regulatory T cell function and reducing inflammation.

Removing autoimmune triggers

We’ve already discussed the role of gluten, iodine, stress and a leaky gut in triggering an autoimmune response. Other potential triggers include estrogens, infectious agents, and environmental toxins.

Estrogen fluctuations can trigger the gene expression of Hashimoto’s in the presence of inflammation and genetic susceptibility. In addition to turning on the genes associated with Hashimoto’s, estrogen surges have been shown to exacerbate the autoimmune attack on the thyroid. This may explain why the expression of Hashimoto’s is so common during pregnancy and perimenopause – both times when estrogen may be fluctuating wildly.

Environmental toxins are associated with autoimmune disease, and Hashimoto’s is no exception. Certain antigens like mercury that bypass our barrier system cause a potent immune response that can become chronic and overactive. If you suspect environmental toxicity may be contributing to your condition, it’s probably a good idea to get a test for chemical haptens and heavy metal antibodies.

Autoimmune thyroid disease has also been associated with a variety of infectious agents, including Rubella, Rubeolla, Epstein-Barr Virus, Retrovirus, Influenza B virus, Coxsakie virus and Yersinia. The mechanism in all cases is theorized to be cross-reaction between thyroid stimulating hormone (TSH) receptors and infectious agents. Once again, if you suspect an infectious agent is involved in your condition, a screening for these pathogens is a good idea.

Enhancing regulatory T cell function

These strategies are all designed to enhance the function of regulatory T cells (also referred to as the Th3 system). Regulatory T cells are used to balance the activity between T-helper cells (Th1 & Th2) and T-suppressor cells (which “turn off” the immune attack).

Vitamin D has been shown to influence regulatory T cells, which in turn modulate T helper cell expression and balance the Th1 and Th2 response. For more on this see The Role of Vitamin D Deficiency in Thyroid Disorders.

The gut flora play a significant role in both cell-mediated (Th1) and humoral (Th2) immunity. Studies show that this protective role can be maintained and modulated by taking probiotics. Specific probiotic strains can influence the secretion of cytokines to help direct naïve helper T cells towards either a Th1 dominant, cell-mediated immune response or towards a Th2 dominant, humoral immune response.

Acupuncture has recently been shown to regulate the Th1 and Th2 immune response. In this study of patients with depression, both Prozac and acupuncture were shown to reduce inflammation. But only acupuncture restored the balance between the Th1 and Th2 systems. In another study, acupuncture reduced inflammation and lessened the symptoms of asthma by regulating the balance between Th1 and Th2 cytokines.

Reducing inflammation

Essential fatty acids (EFAs) play an important role in preventing and reducing inflammation. I’ve written an entire series of articles on this topic, which I’d recommend reading if you haven’t already.

The ideal ratio between omega-6 and omega-3 fatty acids is between 1:1 and 3:1. The average American ratio is closer to 25:1, and as high as 30:1, thanks to diets high in processed and refined foods. The result of this imbalance is – among other things – inflammation.

Two steps are required to bring this ratio back into balance. First, dramatically reducing consumption of omega-6 fats, and second, moderately increasing consumption of omega-3 fats. I explain how to do this in considerable detail in this article.

Another benefit of increasing intake of omega-3 fatty acids is that they have also been shown to help balance the Th1 and Th2 systems.

Aside from ensuring a proper balance of omega-3 and omega-6 fatty acids, following an anti-inflammatory diet/lifestyle and avoiding dietary triggers like gluten and iodine is essential.

Putting these general approaches to balancing the immune system into action should give you a good start towards getting the autoimmunity under control. But if you don’t see the results you’d like, I’d recommend working with someone who knows how to address your particular immune imbalance more specifically.


Tiffany S. August 30, 2010 at 9:33 am

It’s my understanding, as explained to me by a variety of doctors, that Hashimoto’s is NOT hypothyroidism but a fluctuation of hypo and hyper that may or may not eventually result in full-blown hypo. I think explaining it as only hypothyroidism is an over-simplification. I have been able to treat my symptoms with T3 therapy and have very little hypo symptoms anymore and rarely feel the hyper but they had been there. Just my two cents, as a Hashi’s patient.

Chris Kresser August 30, 2010 at 9:44 am

When did I describe Hashi’s as being limited to hypothyroidism?

Elizabeth August 30, 2010 at 6:29 pm

Perhaps you weren’t clear, then, Chris. I had the same belief, but maybe that was because that was what you were discussing.

Chris Kresser August 30, 2010 at 6:37 pm

What I’ve said in the articles was 90% of hypothyroidism is caused by Hashimoto’s.  That’s not the same thing as saying Hashimoto’s is equivalent to hypothyroidism.

Hashimoto’s is an autoimmune disease that progressively destroys the thyroid gland.  During an autoimmune attack, as the gland is destroyed thyroid hormones are dumped into the bloodstream.  This causes a temporary hyperthyroid condition (Hashimoto’s toxicosis), and explains the fluctuations between hypo- and hyperthyroid a Hashimoto’s patient experiences early in their disease.

As time goes on, more and more of the thyroid gland is destroyed and the condition evolves into frank hypothyroidism without any hyperthyroid surges.  Note that some Hashimoto’s patients never experience significant episodes of hyperthyroidism secondary to glandular destruction, while for others, such episodes can be quite severe (to the point of these folks sometimes being misdiagnosed with Graves’).

Ultimately, without (and often even with) treatment all Hashimoto’s patients will end up being hypothyroid.  How much time this takes depends on the person and the treatment.

Maria Minno August 31, 2010 at 1:20 pm

In this article they are taking everything so piecemeal, yet in reality it’s all connected.  I think it’s kind of nearsighted, as opposed to holistic.  If you add it all up, a diet following the principles of Weston A. Price is really what it all points to.  But they never really add it all up.  It’s sort of like if you describe all the letters in detail but you never say the word.  I don’t see anything simple here!  Also, for most of the practitioners I know who have worked with thyroid disease, they believe that iodine will help even autoimmune thyroid disease.  However, this article says to avoid iodine.  I found than in my case, even though I had an autoimmune thyroid condition and was allergic to iodine, a simple anti-allergy procedure (and a healthy diet) enabled me to take the iodine I needed and recover from thyroid problems without any drugs.

Renee Blancq September 1, 2010 at 3:22 pm

“In the first post in this series, we established that hypothyroidism is an autoimmune disease (called Hashimoto’s) in the vast majority of cases. ”

Just to be clear, the above quote from this article is wrong, hypothyrodism is not an autoimmune disorder, Hashimoto’s is an autoimmune disorder with hypothyroidism being the most common symptom of the disorder. Hypothyroidism can be caused by many things but Hashimoto’s is the leading cause of hypothyroidism.

Chris Kresser September 1, 2010 at 3:28 pm

There was a word missing. It should read: hypothyroidism is *caused* by an autoimmune disease in the vast majority of cases.

claire September 3, 2010 at 9:14 pm

I’ve been following this series with interest since my N. Doc has me on iodine supplements and is using iodine loading test(s) to check on my progress. Your anti-iodine ideas gave me food for thought, but no real idea if I should stop taking it. What is the test I should ask for from the Naturapath to determine Hasimoto’s. (I know I haven’t had it)
Also in this article you mention estrogen fluctuations  as a potential auto-immune trigger, but no ideas what to do. This is what my naturapath is helping me with- perimenopausal estrogen dominance and better clearing of estrogen through the liver by working on diet, stress, and helpful supplementation. (she uses estrogen metabolism tests to see how well my liver is doing) I do love your writing, but I can’t help but feel like few doctors, natural or otherwise, do more than just attribute problems like this to perimenopausal hormone imbalances without the corresponding suggestions of tests or treatments.
I’m trying to prevent myself form developing autoimmune disease and it’s frustrating because when hormone fluctuations are a problem, it’s like I’m supposed to accept this as part of perimenopause and that nothing can be done.
Please talk a bit about things women might do about hormone triggered autoimmune disease?

Chris Kresser September 4, 2010 at 9:55 am

Claire: I wish I could give you an easy answer. But these are complex problems, and they’re not amenable to canned, one-size fits all approaches. I couldn’t hope to advise you or anyone else without doing a full work-up and exam to determine the exact mechanisms involved. Hopefully that’s what your naturopath is doing. In general, hormone problems are secondary to (caused by) blood sugar imbalances, adrenal stress (cortisol dysregulation), essential fatty acid deficiencies, hormone clearance issues and gut infections or inflammation. If all of those issues are addressed, the hormones generally balance themselves. In particular, the state of the adrenals is important in perimenopause and menopause because during that time ovarian production of hormones is declining, and the slack is picked up by the adrenals. A salivary test can give your practitioner important information about your adrenal health, and cues for where to go from there.

hans keer September 8, 2010 at 3:55 am

Hi Chris, This is really becoming a helpful series. I forwarded your posts to some acquaintances of mine, who suffer from hypothyroidism. Won’t be long and Kharrazian can serve his apprenticeship with you :-) . This week I wrote an easy to read post on how to reverse a leaky gut and stop autoimmune diseases. I hope your readers may benefit from it too: . VBR Hans

Laurie September 17, 2010 at 8:51 am

Chris – I just found your blog last night and have found it to be extremely informative, and I can’t thank you enough for taking the time to answer people’s questions about these subjects.  I just finished reading Dr. Kharrazian’s book, after looking for years for suggestions to address the underlying cause of my Hashimoto’s.  I thought the book was a good start, but I really wish he had addressed more of the “how to” along with the “why to”.  The recurring theme seemed to be “find a professional who follows these courses of treatment”.  Well, thus far I haven’t been able to find anyone in the area with a clue, plus my insurance doesn’t cover preexisting conditions for the first year of coverage, so I am on my own for a bit.
So, my questions to add to the mix:  Are you aware if preparations such as soaking or fermenting change the gluten in grains to any extent as to make them less inflammatory?  (Nourishing Traditions type prep.)  I’ve read that sourdough bread is better for diabetics than non-fermented breads, so I was wondering if there might be any similar advantage.
Second, what about do-it-yourself probiotics as an aid to build proper gut bacteria to improve the T4 to T3 conversion process?  I culture and consume water kefir, milk kefir, kombucha and yogurt regularly.
Do you feel that a GAPS type diet is required, or is Paleo style enough?  I think my guts are pretty healthy, and don’t seem to react to a lot of the foods on the GAPS list (as far as I know).  My thyroid hormone levels test within high normal range, but I did test positive for Hashi’s.  Overall symptoms are minor (some fatigue, dry skin, cool extremities, aches).  I lost around ten pounds by increasing my fat consumption, and have lost another five or so by reducing carbs, so am very curious about all of this.

Chris Kresser September 17, 2010 at 9:08 am

Laurie: soaking or fermenting grains does improve their digestibility, but it doesn’t eliminate the gluten. I recommend that all people diagnosed with Hashi’s avoid gluten completely, regardless of whether they notice a reaction. We now know that gluten intolerance can manifest in many ways, and gut inflammation is only one of them.

Fermented foods are an excellent way to get probiotics, but make sure you’re getting prebiotic foods as well. These would include resistant starches contained in sweet potatoes, taro, etc. as well as inulin in onions, chicory, jerusalem artichoke, etc. You can also take a prebiotic supplement to see if that helps.

The reason Dr. K says “find a practitioner” is that autoimmune thyroid conditions are incredibly complex and therefore not easy to self-treat. I will be working with patients at a distance beginning in the next few weeks, so that’s an option if you find you need further help.

Becky October 24, 2010 at 1:40 pm


Here’s a good short video on thyroid:
Not mentioned but I heard on a podcast (kharrazian), that you should get your thyroid antibodies (TH2) tested:   TPO (tyhroid peroxidase), and TGB (Thyroglobulin) . And as Chris writes Autoimmune disorders (TH1) can cause hypothyroidism, and can lead to issues of hair loss, fat metabolism and cholesterol.
However, is it true that insulin surges in men (hypoglycemia?), can look like hypothryoidism symptoms (due to elevated estrogen)?
Also, instead of fasting what about getting rid of gluten, and supplementing with chromium, vanadium, copper, alpha-lipoic acid, mixed tocopherols, biotin, zinc, inositol, licorice, b-vitamins, coq10 (ubiquinol), vitamin d3, magnesium, selenium, Gymnema sylvestre, and conditionally, iodine?


Chris Kresser October 24, 2010 at 7:10 pm


I’ve mentioned thyroid antibodies elsewhere in this series.

Insulin resistance may produce symptoms that mimic low thyroid function, such as fatigue and weight gain.  I’m not sure where your reference to fasting comes from.  I didn’t mention that in the article, and I’m not a fan of extended fasts for most people.

megan November 23, 2010 at 1:42 am

wonderful information. i appreciate how you document studies in order to learn more as well as outside resources/books/blogs etc. please continue doing this.

you challenge even the fringe re supplementation and differential therapy. which is great! there is much to learn and the info collected here is a great place to begin.

thank u!

Saundra February 18, 2011 at 8:43 am

My doctor tells me I have hypothyroidism. She tells me the thyroid is a little low but gives no specifics. This has been going on for about 8 months now. From all of my searching on the internet, I don’t seem to have any of the symptoms…no fatigue, depression, sleepy, etc. To the contrary, I am energetic and feel great. The doctor wants to give me prescribed medicine, which I do not want to take if at all possible.
Do you have any suggestions?

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