Understanding the True Cause of Autoimmune Disease

Understanding the true cause of autoimmune disease

Dr. Amy Myers is a former autoimmune patient who has empowered thousands of people to reverse Hashimoto’s thyroiditis, Graves’ disease, and other autoimmune diseases.

Written by Amy Myers, MD

During my second year of medical school I was diagnosed with an autoimmune thyroid condition and it was honestly one of the most frightening and frustrating experiences of my life. Conventional medicine failed me in my own thyroid journey, and it is my mission to not let it fail you too.

After having my thyroid blown up like Hiroshima with a radioactive thyroid ablation, I went in search of the answers that conventional medicine could never seem to provide – what caused my immune system to rogue and attack my thyroid in the first place, and how could I have reversed my condition naturally?

You see, there’s a huge disconnect between what actually causes autoimmunity and how conventional medicine treats it. If you are frustrated by the conventional medicine approach to your health and well-being like I was, I hope this information will help you discover that there is another way to treat autoimmune disease, and you can reverse your condition.

10 Signs You May Have an Autoimmune Disease

If you are experiencing any of these symptoms, especially a combination of several of them, you may have an autoimmune disease.

  1. Joint pain, muscle pain or weakness, or a tremor
  2. Weight loss, insomnia, heat intolerance, or rapid heartbeat
  3. Recurrent rashes or hives, sun sensitivity, a butterfly-shaped rash across your nose and cheeks
  4. Difficulty concentrating or focusing
  5. Feeling tired or fatigued, weight gain, or cold intolerance
  6. Hair loss or white patches on your skin or inside your mouth
  7. Abdominal pain, blood or mucus in your stool, diarrhea, or mouth ulcers
  8. Dry eyes, mouth, or skin
  9. Numbness or tingling in the hands or feet
  10. Multiple miscarriages or blood clots

Autoimmune Disease: A Disease Of The Immune System

The first thing to understand about autoimmune diseases is that they are a disease of the immune system. If you have an autoimmune disease, somewhere along the way your immune system went rogue and began attacking your own tissues. In some cases it’s your thyroid under attack, in others it’s your intestines, your skin, your brain, your pancreas, or another organ. But no matter what part of your body is under siege, the culprit is your immune system. This means that in order to treat, prevent, and reverse autoimmune disease you’ll need to get your immune system back under control.

However, under our current medical system, autoimmune diseases are not recognized as diseases of the immune system as a whole. Instead they are treated as diseases of particular organs. Unfortunately, that means that there isn’t a unified branch in conventional medicine to treat autoimmune conditions. With cancer for example, we have cancer specialists called oncologists who treat many different types of cancers no matter which organ system they involve. Yes, there are some sub-specialties within oncology, but they typically still fall under one main oncology umbrella.

If, on the other hand, you are suffering from an autoimmune disease, you will see a specialist who focuses on the organ system that is being affected: an endocrinologist for Hashimoto’s, Graves’ disease and diabetes, a rheumatologist for rheumatoid arthritis; a gastroenterologist for celiac, ulcerative colitis and Crohn’s; a dermatologist for psoriasis; and so on. If you have multiple autoimmune conditions, as many people do, you will see several different specialists, each of whom will likely prescribe a different medication. And, there is a good chance that none of these specialists will look at how to strengthen and support your immune system, which leads me to my next point.

Supporting, Rather Than Suppressing, The Immune System

In conventional medicine, the belief is that once you have an autoimmune condition, there’s nothing you can do to reverse it, only ways to manage the symptoms. Managing the symptoms typically involves harsh medications that are aimed at suppressing your immune system. While these medications can be effective at reducing some of the symptoms of the disease, since they suppress the entire immune system, they are not without many unwanted side effects such as fatigue, weight gain, depression, increased infection rates and even cancer.

In contrast, functional medicine sees the body as a whole and works on the principle that the health of one system impacts the health and function of the others. Instead of focusing on disease symptom management, we focus on supporting and strengthening the immune system by getting to the root of why the immune system went rogue in the first place. While there is no known cure for autoimmune disease, I believe that there are five key elements that are at the root of all autoimmune conditions. In my functional medicine practice I have been able to successfully help thousands of patients lower and reverse antibodies, get off their harsh medications, and become symptom free.

What's the real source of your autoimmunity?

5 Underlying Causes of Autoimmune Disease

1. Leaky Gut

The gut is the gateway to health. It houses 80% of your immune system, and you can’t have a healthy immune system without a healthy gut. Thanks to research from Alessio Fassano (and I’ve confirmed it in my own practice), we now know that if you have an autoimmune disease your gut has become leaky, meaning the tight junctions that typically hold your gut lining together have become loose, allowing undigested food particles, microbes, toxins, and more to escape your gut and enter your bloodstream.

All of these particles are recognized by your immune system as foreign invaders, sending your immune system into high alert and triggering a huge rise in inflammation. This continual strain on your immune system eventually causes it to go haywire, and it ends up attacking your own tissues by mistake.

2. Gluten

Gluten contributes to autoimmune disease in three key ways. First, it is the primary cause of leaky gut because gluten triggers the release of zonulin in your intestines, a chemical that tells your gut lining to “open up”. Second, it is highly inflammatory, meaning it stresses your immune system. Thirdly, the gluten protein has a similar chemical structure to some of your body’s tissues (specifically your thyroid), which can lead to molecular mimicry, where your body mistakes your tissues for gluten and attacks them.

3. Toxins

Toxic molds (mycotoxins) and heavy metals such as mercury are the two main toxins I see in those with autoimmune conditions. Mycotoxins are very volatile compounds produced by toxic molds that wreak havoc on the immune system.

We are exposed to heavy metals like mercury in different ways: mercury amalgam fillings in teeth, fish consumption, and the environment. Mercury is toxic to our bodies and can be one piece of the puzzle for those with autoimmune diseases.

4. Infections

Scientists have long suspected that infections from bacteria, viruses, and other toxins were likely to blame for the development of autoimmunity. There are now a number of infections, including Epstein Barr (the virus that causes mono), Herpes Simplex 1 and 2, E. coli, that have been linked to autoimmune diseases.

5. Stress

Levels of stress-related illnesses are on the rise, and stress, both of the emotional and the physical variety, has been shown to trigger and intensify autoimmune disorders. Stress disrupts immune function through several distinct pathways. Stress is the body’s response to a threat–a wound, injury, or infection. Chronic stress (the kind we face in this day and age) leads to long term inflammation that never really shuts off, creating autoimmune disease. Once the autoimmune response is in place, immediate stress only exacerbates it.

5 Steps to Reverse Autoimmune Disease Naturally

1. Repair your gut.

Repairing your gut is essential to healing yourself. After all, nearly 80% of your immune system lies in your gut! Functional medicine practitioners use the 4R approach to repair your gut by removing the bad elements (toxic and inflammatory foods and gut infections) that damage your gut, restoring essential elements for proper digestion, reinoculating your gut with good bacteria, and repairing your gut lining.

2. Remove gluten, grain, and legumes from your diet.

For my patients with autoimmune diseases, I highly recommend removing not only gluten but all grains and legumes from their diet. These foods contain proteins known as lectins, which act as a natural pesticide for crops and can wreak havoc on the lining of your gut. Many of my patients find that most, if not all, of their symptoms disappear simply by optimizing their diets to support their immune systems!

These Zucchini Muffins are my go-to baked goods when we have friends or family over for breakfast. They are so fragrant with cinnamon and nutmeg, you are going to LOVE them!

The Autoimmune Cookbook

3. Test for heavy metals and mycotoxins.

I recommend having your MTHFR genes tested and doing a DMPS chelation challenge test through a functional medicine practitioner to determine if mercury or other heavy metals are an issue for you. Also test to determine if you are being exposed to mycotoxins. I recommend that all my patients find a biological dentist to remove their mercury amalgam fillings.

4. Find and treat infections.

There are a number of bacterial and viral infections that have been associated with autoimmune conditions. Have your doctor test for infections such as HSV and EBV. Monolaurin from coconut oil can be a very effective treatment for both HSV and EBV. Lysine and a lysine-rich diet is effective at treating HSV infections.

5. Manage your stress.

With our modern lives we should all be prioritizing stress reduction. Take care of yourself by adopting some stress-relieving strategies such as exercise, meditation, art or whatever helps you relieve stress. The key is to find a few practices that work for you and stick with them. Even giving yourself five minutes to sit quietly with a fragrant cup of herbal tea (caffeine-free, of course!) can help tremendously.

My approach is based on getting to the root of the problem: removing the elements that derailed your immune system in the first place and strengthening your immune system rather than suppressing it. That’s why using this approach enables you to reverse and prevent many different autoimmune conditions at once.

About Amy Myers, MD

After serving 2.5 years in the Peace Corps in rural Paraguay, I decided to become a doctor. During my second year of medical school, I was having panic attacks, tremors, and insomnia. I was diagnosed with Graves’ disease, an autoimmune disease in which my thyroid was attacking itself and causing it to become overactive.

I first did nothing. I then tried Chinese Medicine and was eating lots of fermented foods, whole grains, and terrible tasting powdered herbs. That did not help at all.

I finally decided to do the conventional medicine called PTU, which inhibits my thyroid from making so much hormone. After a few weeks, I felt terrible. I returned to my doctor for lab testing and found that my liver was being damaged by the medication and I had something called toxic hepatitis. I was ordered to stop the medication and to strict bed rest. Fearing for my health, my life, and the possibility of having to drop out of medical school, I opted to have my thyroid ablated.

I never want anyone to go through what I had to go through, so it is my mission to educate as many as I can that there are other healthier ways to recover from thyroid disease. Visit me online at Amy Myers MD [dot] com.

READ NEXT: Why Caring for Your Liver is Key to Healing from Hashimoto’s

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I appreciate every share! Thank you.

About Dana Trentini

Dana Trentini founded Hypothyroid Mom October 2012 in memory of the unborn baby she lost to hypothyroidism. This is for informational purposes only and should not be considered a substitute for consulting your physician regarding medical advice pertaining to your health. Hypothyroid Mom includes affiliate links including the Amazon Services LLC Associates Program.


  1. Fiammetta Rubin N.D.— I heard you—Went through it all. for years using Chinese medicines which really helped, but the study can be long.–Then ,4 years ago my stress was so intenseMy eyes had become the spouts of a water fountain.There was a divorce, two moves, loss of my books, thefts in my apartment., from which I had to throw out about 200 books( fire danger)…Anyway, it took me about two or three years to realize that stress, various ” diseases” occurs because we have become afraid of life itself and what it may bring us.—Finally I decided to change my “conscious mind” and FOCUS on positive, joyful, loving . Our bodies are driven by emotions . If we can let go of fear, hate, anger and look at life as a garden where we can survive with others which at times ARE VERY DIFFERENT THEN US, and accept them in their difference, unconditionally, difficult relationships where dialogue is the key as heart opens, shall allow trust, need for joy, SELF LOVE. , SELF ESTEEM, and SELF RESPECT. towards ourselves and OTHERS. THEY shall allow us to be open and express our thoughts and emotions as we share them . Dialogue , sharing with one another our joy of life, even as minuscule, is the only cure , because loneliness and separation from life are the major catalysts of misery.
    Find beauty in a blade of grass, in the wagging of a dog’s tail, in the eyes of the beloved, etc… and life shall follow because you have opened your door to it.– Namaste.

  2. Lois Miller says

    *chronic fatigue, not chronic depression

  3. Lois Miller says

    I was diagnosed with Hashimoto thyroiditis in mid 90s. Began low dose of synthroid. Never lost an ounce of the sudden gain of 20 lbs. Debilitating fatigue has been, and continues to be my chief complaint. Dosage has been increased a couple of times, now on 125 MCG. Endocrinologists have all said my fatigue is most likely due to depression. Who wouldn’t be depressed with chronic depression and inability to lose weight? Interesting that I have Herpes I and II, EBV, and CMV. I believe these play a part in symptoms. Sure would love to feel better.

  4. Pamela Morris says

    I have MS, my other had MS and died at age 74 of thyroid cancer. My son came down with Hashimoto’s and so did I after diagnosed and then had no symptoms. I am the poster child that it’s not the food because I eat really well and know what were void since I heard when diagnosed to stay off gluten; grains lectins(beans), all. Flour Products,Really watch dairy, tons of fruits and vegetables.
    My son got had Hashimoto’s and what can I do to prevent him from coming down MS someday from what we know now, which I know isn’t much and he’s a boy whose parents got divorced and his father is doing parent alienation of me . I really think this ugly divorce has pulled out whatever gene may have been in me. I believe what I’ve been going through a betrayal really pulled out whatever may being me what with doctors are not testing. There’s no way to do a double blind study

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