In 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.

I often get comments and emails from people asking me which thyroid hormone I think is best. My answer is always the same: “It depends.” As much as some practitioners would like to make us believe, there is simply no “one size fits all” approach to thyroid hormone replacement.
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Note: This will be my last post until the end of August. My wife and I are going up to the Sierras to hike and soak in the hot springs for a few days before the big acupuncture licensing exam next Tuesday. The day after that we head to southern Mexico to surf and relax on the beach for a couple of weeks.
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According to the American Association of Clinical Endocrinologists, 27 million Americans suffer from thyroid dysfunction – half of whom go undiagnosed. Subclinical hypothyroidism, a condition in which TSH is elevated but free T4 is normal, may affect an additional 24 million Americans. Taken together, more than 50 million Americans are affected by some form of thyroid disorder.
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I just wanted to take a moment to welcome readers from 


