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Causes of Chronic Fatigue Syndrome

Causes of Chronic Fatigue Syndrome was Written by Dr. Diane Mueller

So you have chronic fatigue syndrome? Now what?

For too many people the diagnosis is the end, instead of the beginning.

Chronic fatigue syndrome (CFS) is a complex condition that is characterized by extreme fatigue that persists for at least six months and is not relieved by rest. The cause of CFS is not fully understood, but there are several things that we have seen both in research and in clinical care that are the underlying reasons for chronic fatigue syndrome. In this blog, we will discuss some of the possible causes of CFS, including thyroid, adrenal, gut problems, nutrient deficiencies, mold, and hidden infections.

causes of chronic fatigue syndrome

The biggest thing to be aware of is that there is a reason why you have chronic fatigue syndrome. The right tests need to be run and not all of them can be run through your regular doctor. We help our clients get the tests they need to get answers! Book a free discovery call with us to learn more about if we can help you!

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More on Causes of Chronic Fatigue Syndrome

The thyroid plays a big role in chronic fatigue syndrome for many people

The thyroid gland is a crucial endocrine gland that is responsible for regulating the body’s metabolism. When the thyroid gland is not functioning properly, it can lead to fatigue, weight gain, and other symptoms that are commonly seen in CFS. Hypothyroidism, a condition where the thyroid gland does not produce enough thyroid hormones, is a potential cause of CFS. The diagnosis of hypothyroidism can be made through a blood test that measures the levels of thyroid hormones. Although one of the problems is that people can have labs that show up as “normal” but the thyroid is still not functioning optimally. It is important to work with clinicians who run a full thyroid panel (more than just a TSH) and really understand proper diagnosis.

Adrenal Imbalances:

The adrenal glands produce hormones that help the body cope with stress. When the adrenal glands are not functioning properly, it can lead to fatigue and other symptoms commonly seen in CFS. Adrenal fatigue,  a condition where the adrenal glands are producing incorrect amounts of hormones a potential cause of CFS. Adrenal fatigue is not a real medical term as the adrenal glands do not actually get tired and stop working. What happens is there is a disconnect between the brain and the signal to the adrenal glands. The brain fails to signal to the adrenal glands to produce the right amount of hormones and the individual develops fatigue as a result. Testing for cortisol and DHEAs can be helpful markers to measure adrenal function.

Other Potential Cause of Chronic Fatigue Syndrome:

Gut Problems:

The gut is home to trillions of bacteria that play a crucial role in the body’s immune system and overall health. When the gut is not functioning properly, it can lead to inflammation and other symptoms that are commonly seen in CFS. Leaky gut syndrome, a condition where the lining of the gut becomes permeable, allowing toxins and other substances to enter the bloodstream, is a potential cause of CFS. The diagnosis of leaky gut syndrome can be made through a blood tests that measure things such as zonulin and LPS antibodies.

Nutrient Deficiencies:

Nutrient deficiencies can lead to a wide range of symptoms, including fatigue, muscle weakness, and brain fog, all of which are commonly seen in CFS. Nutrient deficiencies that have been linked to CFS include deficiencies in vitamin D, vitamin B12, magnesium, and iron.  Blood tests are not also accurate for many nutrients. B12 is often most accurate using a test called MMA. Magnesium is best tested using a test called the organic acids. When testing iron, make sure to run a full iron panel and not just a serum ferritin (which many doctors do). Ferritin is a very sensitive marker and can be impacted by inflammation. Because iron is one of many things that impact ferritin levels, it is a commonly used but poor iron marker.


Mold is a type of fungus that can grow in damp and humid environments, such as basements, bathrooms, and kitchens. When mold spores are inhaled, they can lead to respiratory symptoms, including fatigue, muscle weakness, and brain fog, all of which are commonly seen in CFS. Use the urinary mycotoxin tests for informaiotn on mold in the body. Mold can cause chronic fatigue symptoms as well as other widespread issues in the body. For more on mold symptoms, see our blog HERE.

Hidden Infections:

Hidden infections, such as Lyme disease and Epstein-Barr virus, can lead to fatigue and other symptoms commonly seen in CFS. These infections are often difficult to diagnose and require specialized testing, such as PCR and Western blot testing. We strongly recommend a company called vibrant wellness which has the most thorough testing on the market for hidden infections. Like mold, Lyme and other chronic infections can cause not only chronic fatigue, but a wide variety of other symptoms. See our blog HERE for more information about Lyme Disease and all it causes.

For more information on Black Mold Symptoms See our Blog Below


  1. Nacul, L. C., Lacerda, E. M., Campion, P., Pheby, D., Drachler, M. D. L., Leite,
    J. C., … & Poland, F. (2008). The functional status and well-being
    of people with myalgic encephalomyelitis/chronic fatigue syndrome and
    their carers. BMC Public Health
    , 8(1), 1-11.
  2. Scott, L. V., Salahuddin, F., Coomber, E., & Dinan, T. G. (1999). Altered adrenal function in chronic fatigue syndrome. The Journal of Endocrinology, 184(2), 387-391.
  1. Marques, C. D. L., Ferreira, R. C., Kemp, R., Teixeira, L., Souza, É. C., & Teixeira, M. M. (2017). Vitamin D, vitamin B12, and ferritin in patients with chronic fatigue syndrome and fibromyalgia: a systematic review and meta-analysis. Revista Brasileira de Reumatologia
    (English Edition), 57(2), 163-169.
  1.  Brewer, Joseph; Thrasher, Jack. Detection of Mycotoxins in Patients with Chronic Fatigue Syndrome. Toxins. 2013 Apr 11. doi: 10.3390/toxins5040605
  1. Bruce M. Carruthers et al. Journal Of Chronic Fatigue Syndrome Published online: 4 Dec 2011

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The Causes or Mechanisms of Action

Despite the sometimes-similar symptoms, the MOAs of these two conditions are very different:

  • Lyme Disease is caused by the bacteria Borrelia burgdorferi and Borrelia mayonii. Lyme is a bacterial infection.
  • The cause of Fibro is much less clear and could involve genetic, hormonal or other factors. Gut health may play a role too. But the primary MOA is thought to be a dysfunction of pain sensitization. You can read more in our FM blog here.  
  • Fibromyalgia is often triggered by a stressful event, including an infection, trauma (due to an accident, serious injury or divorce) or major surgery. FM can actually be triggered by an infection like Lyme Disease.

What is the Link?

Similar Symptoms & Mis-Diagnosis

  • FM can be mis-diagnosed as Lyme disease.
  • Late-stage chronic Lyme disease can be mistaken for FM.
  • Lyme Disease can trigger Fibromyalgia.

So how do we differentiate between LD and FM?

How do we untangle symptoms and identify a case of chronic Lyme disease vs post-infectious Fibromyalgia?

We need to do a thorough exam, the correct labs and a deep analysis of the overlapping symptoms. There are other things to look at to get a correct diagnosis. These include:

  • A history of a bulls-eye rash, a tick bite or spending time in areas where Lyme Disease has been reported are good indicators that it could well be Lyme.
  • Antibiotics should improve Lyme Disease symptoms, while they don’t help in the case of Fibromyalgia.
  • Pain in specific tender points is associated with Fibromyalgia more than other illnesses.
  • Stiffness in Lyme Disease occurs mainly in the neck and joints. In Fibromyalgia, it is usually widespread pain.
  • Lyme Disease can cause arthritis symptoms and swollen joints, especially in the knees. Fibromyalgia causes pain and stiffness but doesn’t typically involve swelling or damage to the joints.

In our clinic, we have expertise in treating a range of complicated, difficult-to-diagnose conditions like Fibromyalgia and Lyme Disease. We look for the root causes in our patients to identify what could be causing the symptoms. We regularly treat and resolve Lyme, chronic infections and other complex conditions in patients in our Functional Medicine clinic.

Have Lyme Disease or suspect that you do?

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people restore their health
and quality of life by diagnosing
and treating their Lyme Disease.

“Dr. Mueller’s approach to medicine is refreshing! There is only so much you can do with western medicine and in my life I was needing a new approach.  By addressing the whole body, nutritional diet factors, environmental factors, blood work, and incorporating ideas I had not previously known, I was able to break through with my conditions.  I am not only experiencing less pain in my life, but through the process of healing guided by Dr. Diane Mueller, I am now happy to say I have more consciousness surrounding how I eat, what to eat and when things are appropriate.  Living by example Dr. Mueller has a vibrancy that makes you want to learn and know more about your body and overall health.  I highly recommend her to anyone looking for new answers, a new approach to health, or in need of freedom from pain and limitations.”

-Storie S.

Kihei, HI

Lyme Disease is Often Misdiagnosed as Fibromyalgia, Chronic Fatigue, Depression,
or Other Illnesses

Have Mold Illness or Lyme Disease or suspect you do?

We have helped thousands of people restore their health and quality of life by diagnosing and treating their Mold Illness, Lyme Disease and other root causes.

End Chronic Fatigue, Pain, Brain Fog &
More Taught By Expert Dr. Diane Mueller