10 Root Causes of Fibromyalgia (#3 is Thyroid)

10 root causes of fibromyalgia (#3 is thyroid)

You can’t imagine how many readers reach out to me about chronic pain and fibromyalgia. If your doctor dismisses thyroid as a possible culprit for your pain, bring them this article.

Written by Amy Myers, MD

It is estimated that fibromyalgia affects nearly 6 million or 1 in 50 people. Fibromyalgia is classically characterized by chronic pain particularly muscle pain, fatigue, sleep disturbances, brain fog or cognitive impairment, depression and painful tender points throughout the body.

Conventional medicine has yet to uncover the cause of fibromyalgia and only offers management of symptoms through pain medications and antidepressants.

Functional medicine, on the other hand looks to find the root cause of fibromyalgia and other chronic diseases, treating the problem at the root level thereby restoring the patient to health. As a functional medicine physician, I have helped many patients recover from fibromyalgia. Below are the top ten root causes of fibromyalgia I see in my clinic.

10 Root Causes of Fibromyalgia

Gluten Intolerance:

Gluten has been linked to more than 55 diseases and is often called the ‘big masquerader’. The reason for this is that the majority of symptoms of gluten intolerance are not digestive in nature but rather neurological such as pain, cognitive impairment, sleep disturbances, behavioral issues, fatigue and depression.

Candida Overgrowth:

Candida is a fungus or yeast, and a very small amount of it lives in your intestines. However, when overproduced, candida breaks down the wall of the intestines and penetrates the bloodstream, releasing toxic byproducts into your body causing a host of unpleasant symptoms such as brain fog, fatigue, digestive issues and pain. Virtually every one of my patients with fibromyalgia has had Candida overgrowth.


More than half of the people with thyroid issues have no idea they have one and 90% of these have hypothyroidism, or an underactive thyroid gland. It is vital that your doctor check six different blood markers – TSH, Free T4, Free T3, Reverse T3, Thyroid Peroxidase Antibodies and Thyroglobulin Antibodies – to measure your thyroid gland’s function. It’s imperative that your doctor use the optimal levels rather than the standard reference range when assessing and diagnosing thyroid disorders. Getting my patient’s thyroid levels into an optimal range, typically alleviates their fatigue, brain fog, sleep disturbances and depression.

Vitamin Deficiencies:

Magnesium, vitamin D, and B12 deficiency are the most common vitamin deficiencies I see in those who have been diagnosed with fibromyalgia. I have had several patients completely reverse their fibromyalgia symptoms with magnesium alone. The best way to measure magnesium is a red blood cell (RBC) magnesium level, which can be tested through any conventional lab.

Small Intestine Bacterial Overgrowth (SIBO) and Leaky Gut:

There are more bacteria in us and on us then there are of our own cells. When these bacteria get out of balance through use of antibiotics or a sugar-rich diet we can lose our ability to digest and absorb nutrients, particularly B12. Gluten can cause SIBO and leaky gut and SIBO and leaky gut can lead to gluten and other food intolerances. It’s a catch-22 and a vicious cycle. You must ‘fix the gut’ first in anyone with fibromyalgia or any chronic illness.

Adrenal Fatigue:

Adrenal fatigue is a result of the chronic stress whether real or perceived. Chronic pain is a stress to the adrenal glands, though typically not the initial adrenal stressor. The initial stressor is usually something such as food intolerances, Candida, mercury toxicity, vitamin deficiencies or mycotoxins. My goal is to support the adrenals with adaptogenic herbs while we search for the root cause of the stress and correct it.


Mycotoxins are very toxic substances produced by toxic molds. Only about 25% of the population carries the genes to be susceptible to the effects of mycotoxins.

Mercury Toxicity:

I recommend that all my patients find a biological dentist and have their mercury amalgam fillings removed. Mercury is toxic to our bodies and can be one piece of the puzzle for those with fibromyalgia and other chronic illnesses such as chronic fatigue syndrome, autoimmune diseases, neurological disorders and cancer. I then recommend heavy metal testing using a pre and post DMPS urine challenge test.

MTHFR Mutations:

This is a genetic test you can get though any conventional lab. The more mutations you have at the MTHFR gene the less able you are to methylate and detoxify particularly toxins such as mercury and lead. The more mutations you have at this gene the higher your requirements for methyl-B6, methyl-B12 and folinic acid in order to keep your detoxification pathways working properly.

Glutathione Deficiency:

Glutathione, a molecule, is the most critical part of our body’s detoxification system. Glutathione gets recycled in our body unless our toxic burden gets too high or we lack GSTM1 and GSTP1, the enzymes needed to recycle and produce glutathione. Taking glutathione or the precursors (NAC, alpha lipoic acid, milk thistle) often helps my patients dramatically with fatigue.

As you can see from the above list, many of these causes are interrelated and often there is no one single root cause to fibromyalgia or any chronic illness. It is a combination of several or possibly all of the above. Because getting to the root cause can be complex, I recommend that you find a functional medicine physician in your area to help uncover the root cause for you. You do not need to suffer needlessly or mask your symptoms with pain medication and antidepressants. There are doctors like myself who can help you!

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. I’ve seen incredible health changes with my patients in my clinic Austin UltraHealth.

READ NEXT: When hypothyroidism is painful: Musculoskeletal manifestations

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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. Terri Geiselman says

    Hi, I have been diagnosed with both hyperthyroidism and hypothyroidism. Originally I was just being treated for hypothyroidism. I accidentally ended up in the hospital with clinical hyperthyroidism due to a medicine mix up, my levels went way too high. My TSH levels have not rebounded sonce. I am on methimazole, my doctor says my T4 is normal but I feel awful. I have been fighting against having an ablation. I gained tons of weight(over a hundred pounds) while having hyperthyroidism. What steps can I possibly take to bring by TSH levels back in range? Do I have any options other than ablation?? I am scared. I cant gain more weight I am already over 300 lbs. I also have had fibromyalgia since at least my early 20’s , possibly ME/CFS too. I don’t know what to do.
    Can you give me any guidance. I feel horrible and I am sure it is my thyroid causing it.

  2. Catherine Dee says

    Hi Louisa,
    I to have just stumbled across this article. I have a recent diagnosis of fibromyalgia. I was diagnosed with hypothyroidism a few years ago coupled with degenerative disc disease, early hysterectomy and parathyroidectomy, severe vitamin D deficiency. I have seen several drs. Over the years and it is difficult to find one that listens to you. My advice is to keep all your test results and compare them yourself with research and be armed with all your own data when you see your doc. It’s the only thing that has helped me get answers. If they don’t listen to you get a new doctor!

  3. Angela Weiss says

    Hi, I’ve been diagnosed with hypothyroidism and fibromyalgia for years. I’ve had ups and downs, currently it’s more of a down I just don’t feel right and my labs are horrible. I did have labs done by another doctor (for something else) and one of them said I have a MTHFR mutation, but no one knows what that means. Is this something that could be effecting me?

    • Melissa Cole says

      Yes it can affect you! I have it. Depending on which mutation you have you may not be absorbing vitamin b12 , vitamin d or folate. All of which will make you feel terrible if they are low.

  4. Chandra Dyer says

    I was diagnosed with Fibromyalgia around 2007-2008, so then the treatment began to try to “help” with my symptoms. Shortly after my last child was born in 2009, I was diagnosed with hyperthyroid and ended up having an ablation done. I am now bouncing back and forth between “normal” numbers and being hypothyroid. The fatigue, muscle and joint pain, sleepless nights and much more wear me out. I am now wondering if it was my thyroid all along and do you have any suggestions to help. Thank you so much!

  5. I left a long comment about my story with gluten, thyroid, Fibromyalgia and other autoimmune diseases and was a bit shocked when your site said it was spam and deleted it!

    • Hi Lee, The comment plugin that I use at Hypothyroid Mom automatically deletes what it detects as spam although sometimes I find comments in my Spam folder that are definitely not spam and uncheck it. You can’t even imagine how many hundreds of spam comments from hackers try to get past my comment spam filter. It makes having a comment section on my site very challenging. I didn’t notice a comment from you in my spam file. What was your comment? I would love to hear it.

    • Hi Lee, I had set up a plugin to protect the comments on my page because the number of spam comments was outrageous. I’m sorry if your comment was deleted but it wasn’t done by me. If it included a link that may be why. Please retry without any links.

  6. Louisa Case says

    I have only stumbled on this article today as I am convinced I have been suffering from fibromyalgia. I have ALL the symptoms I have was first diagnosed with hyperthyroidism in my early 20s and now in my 40s I am hypo.. The dilemma I have is how do I g9 about telling a doctor his or her job .??

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