When Your Whole Body Hurts: Understanding Underlying Causes of Fibromyalgia

A Person Holding Their Head in Pain

Fibromyalgia is a common condition that presents with widespread muscle and joint pain, fatigue and trouble thinking clearly (Bhargava 2021). People that struggle with the condition also commonly have irritable bowel syndrome, thyroid problems, headaches and migraines, temporomandibular joint pain (clicking or pain with opening and closing the mouth), interstitial cystitis (pain and irritation of the bladder), insomnia, sleep apnea, anxiety and depression.   

Fibromyalgia is a condition that is not well understood. Unfortunately, to this day, you still find doctors that deny the existence of the condition. This outright denial can further traumatize a patient who is already suffering. However, by understanding and addressing some of the underlying causes of fibromyalgia, it is possible to help reduce symptoms. 

Potential causes of fibromyalgia include:

  • Digestive problems and gut flora issues
  • Hypothyroidism
  • Insomnia and sleep apnea

Digestive Problems and Gut Flora Issues

Fibromyalgia has a clear association with digestive problems. Irritable bowel syndrome and other digestive complaints have consistently been found to be more common in fibromyalgia patients (Erdrich 2020). 

While the research is in its infancy, changes in gut flora and other aspects of the digestive tract have been noted in the condition. While some results have been mixed, patients with fibromyalgia have been found to have higher rates of celiac disease, a potentially life-threatening sensitivity to wheat gluten and related products (Nisihara 2016). For any fibromyalgia patient that has severe digestive symptoms, evaluation of celiac disease and appropriate treatment may be helpful (Rodrigo 2013). 

Interestingly, fibromyalgia patients may also be reacting to wheat and gluten without having celiac disease. One trial of patients testing negative for celiac disease found large improvements in fibromyalgia symptoms for more than one-third with a gluten-free diet (Isasi 2016).  

An earlier study found that 100% of patients with fibromyalgia tested positive on breath testing for small intestinal bacterial overgrowth (Pimentel 2004). And increases in intestinal permeability—or leaky gut—have been found in fibromyalgia patients (Goebel 2008). Increased intestinal permeability allows undigested food particles to potentially pass into the body and activate an immune response.

Evaluating the bacteria in the digestive tract of fibromyalgia patients has also revealed differences from healthy individuals. The differences in bacteria that were identified have potential effects that might be related to fibromyalgia symptoms (Minerbi 2020).

Hypothyroidism and Fibromyalgia

Fibromyalgia is a “diagnosis of exclusion.” In other words, you have to evaluate every other possible cause of the patient’s symptoms before diagnosing fibromyalgia. If no other cause can explain the symptoms then you can consider diagnosing fibromyalgia. 

One of the known conditions that can mimic symptoms of fibromyalgia is hypothyroidism. The thyroid gland is located in the front of the neck and releases thyroid hormones. These hormones set the pace at which the body functions. If you have too little thyroid hormone—hypothyroidism—the body slows down and symptoms can emerge. 

The symptoms of hypothyroidism include fatigue, depression, constipation and dry skin. A subset of patients—somewhere between 25% and 79%—also present with muscle and joint pain, cramps, stiffness and weakness (Anwar 2010). Pain symptoms that are due to hypothyroidism, with proper treatment, typically resolves in three or four months (Duyff 2000).    

Unfortunately, thyroid problems are common in fibromyalgia patients, yet often missed. One study found around 12% of patients diagnosed with fibromyalgia had outright thyroid disease that hadn’t been previously identified. An additional 38% had evidence for an autoimmune thyroid condition (Nishioka 2017).  

Insomnia and Sleep Apnea

When people don’t get enough sleep, their sensitivity to pain increases (Haack 2012). It’s been hypothesized that poor sleep can lay the foundation for chronic pain and fibromyalgia (Martinez 2014).

One cause of poor sleep is sleep apnea. Sleep apnea is a condition where the upper airway in the throat collapses during sleep getting in the way of breathing. Common symptoms include snoring, waking up gasping or choking, daytime sleepiness and having a dry mouth or sore throat in the morning. One recent study found that 66% of women with fibromyalgia had sleep apnea, likely making their pain worse (Mutlu 2020). An earlier study found that 50% of fibromyalgia patients had sleep apnea and improved significantly with sleep apnea treatment (Koseoglu 2017). 


Fibromyalgia is a complex condition that is not well understood. However, evaluating for celiac disease or other digestive problems, thyroid dysfunction and sleep apnea can likely benefit a significant proportion of patients. Considering the long-term pain and suffering often produced by the condition, treating known factors that cause or worsen fibromyalgia pain could go a long way towards providing symptomatic relief. 

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