Surprising Causes of Chronic Pain (And How To Get To the Root)

Chronic pain is one of the most common symptoms we see in our telehealth functional medicine practice. 

For many patients, it’s both confusing and frustrating. Doctors often dismiss unexplained pain instead of looking for answers. And the answers themselves can be complicated—as with other nonspecific symptoms like fatigue, chronic pain is almost always multifactorial (brought on by a combination of different factors). 

Our job is to untangle these causes, get to the bottom of the problem, and heal aches and pains from the source. Here are some of the most common causes we see (which might surprise you), and how to determine what might be going on in your case. 

An Interconnected, Functional Medicine Perspective On Chronic Pain 

Sometimes, chronic pain is the direct result of an injury. You’ll want to look at things differently if you remember an acute cause of your pain (like falling and hitting your knee, or pulling a muscle in yoga), or if your pain is really specifically occurring in one spot. 

But if you’re experiencing chronic pain and you don’t know why, it’s important to consider the interconnected nature of the body. 

While conventional medicine tends to separate out individual systems and parts of the body and treat them differently, the reality is that the gut, brain, and the rest of the body are deeply intertwined. A functional medicine approach considers gut health, mental health, and biological, social, and psychological factors that may come together to cause pain.  

Instead of just treating all pain as the same, and recommending painkillers (which can exacerbate many of the actual underlying causes of the problem), we look at what’s going on beneath the surface with every unique individual. 

READ MORE: Is Ibuprofen Bad For You? The Truth About NSAIDs and Your Gut Health 

With that in mind, here are some of the most surprising and common causes of chronic pain. 

Gut Dysbiosis, Leaky Gut, or Intestinal Inflammation 

Like so many chronic symptoms, pain often comes back to the gut. Gut dysbiosis (an imbalance between beneficial and harmful bacteria in the gut), increased intestinal permeability (leaky gut), and small intestinal bacterial overgrowth (SIBO) can all contribute to systemic inflammation, which can trigger symptoms including chronic pain. 

Many of the neurotransmitters involved in pain regulation are also made and stored in the gut. Imbalances in the gut can disrupt the production and balance of these neurotransmitters, affecting pain perception. (1) 

Recent research has demonstrated the connection between gut dysbiosis and pain including in fibromyalgia, with the severity of a person’s pain correlating to the severity of their bacterial dysbiosis. (2, 3) 

Emotional Trauma and Chronic Stress

It’s essential to look closely at the mind-body connection when it comes to chronic pain. 

Pain affects us on physical, neurological, and emotional levels. Chronic stress, unresolved trauma, and deeply internalized shame can all recalibrate the nervous system in ways that heighten pain sensitivity. (4) 

Emotional pain from past trauma that hasn’t been processed can also show up as chronic physical pain. Pain and depression are linked by their common inflammatory pathways, and we know that people with chronic pain are more likely to experience depression, anxiety, and other mental health conditions. (5) 

Chronic stress also raises cortisol levels, which can drive or exacerbate inflammation throughout the body, leading to increased levels of pain. 

This is why it’s so important to create safety in the nervous system in order to heal chronic pain (rather than just suppressing symptoms, which often doesn’t work for those who have unresolved trauma at the root of the problem). 

READ MORE: Understanding The Overlooked Connection Between Chronic Pain + Mental Health | Dr. Will Cole 

Food Sensitivities 

Hidden food sensitivities are an often overlooked culprit behind chronic pain. Food sensitivities differ from allergies in several ways, including that reactions are often delayed, making them challenging to pinpoint. 

Foods you’re sensitive to, which may include gluten, dairy, eggs, high histamine foods, nightshades, legumes, or others, can create gradual, systemic inflammation that causes joint pain, headaches, and stiffness days after consuming the foods. And repeated exposure to those foods can keep inflammatory pathways switched on. 

While we’re here, beyond sensitivities to generally healthy foods, regularly eating inflammatory foods like processed foods and sugar can also contribute to chronic pain. (6) 

Underlying Infection 

Infections don’t always end as cleanly as we think they do. Even after the acute phase has passed, they can leave behind immunological and neurological changes that perpetuate pain. 

Several kinds of bacteria and viruses, including SARS-CoV-2 (the virus that causes COVID), have been shown to trigger immune responses and pain that can linger long after the infection itself has resolved. (7) 

Lingering pain after infection can be caused by molecular mimicry (where the immune system continues attacking tissues that resemble components of the original pathogen), nervous system sensitization, or changes in the microbial environment that directly cause pain. 

Lyme disease is one key example of post-infectious pain. Even after comprehensive treatment, many individuals continue to experience widespread pain, fatigue, and cognitive symptoms. This may result from immune system dysregulation and autoimmunity triggered by the infection, or central sensitization where the nervous system remains hypersensitive to pain signals. (8, 9) 

Toxin Exposure or Buildup 

The many toxins we’re constantly exposed to in modern life, from mold and heavy metals to the chemicals in our cleaning and personal care products to air pollution, can all contribute to chronic inflammation and pain. 

Magnesium Deficiency and Other Nutrient Imbalances 

Pain modulation depends on adequate nutrient status. Magnesium, in particular, plays an essential role in calming neurotransmitters that can cause pain hypersensitivity, as well as supporting muscle and nerve function. (10) Unfortunately, the majority of Americans are not getting enough magnesium through diet alone. 

Other deficiencies, including vitamin D, B vitamins, and omega-3 fatty acids, can also impair our natural inflammation-modulating and repair mechanisms. (11) 

Try Mag18 from Longevity RX, a peptide-powered magnesium complex with vitamin D formulated to work at the cellular level. 

Autoimmunity 

Autoimmunity, whether a specific autoimmune condition has been diagnosed or not, can cause chronic pain through systemic inflammation. While pain is a well-known symptom of certain autoimmune conditions, such as rheumatoid arthritis, autoimmunity anywhere can lead to joint pain and muscle aches. 

Autoimmunity often results from a combination of factors we’ve already talked about, like leaky gut and unresolved trauma, reinforcing the need for a comprehensive approach rather than isolated treatment strategies. 

Sleep Disruption

Sleep is one of the body’s most powerful pain modulators. During deep sleep, the body repairs tissues and modulates inflammation. Without adequate, good quality sleep, we become less resilient and less able to handle pain. (12) 

We also see increased levels of inflammation, which can trigger further pain. Of course, pain makes it harder to sleep, which can lead to a very frustrating vicious cycle. 

How To Get To the Root Cause of Your Pain 

Because chronic pain is rarely driven by one single factor, uncovering the root cause requires some detective work. At my telehealth functional medicine clinic, we often recommend specialized testing to help identify hidden contributors like autoimmunity, nutrient deficiencies, gut imbalances, toxic burden, and food sensitivities. 

We combine these test results with a thorough health history and understanding your unique health profile. 

Other strategies that can help determine what’s going on include doing an elimination diet to identify food sensitivities, and investigating your diet in general to see if you may be lacking certain nutrients or consuming a lot of inflammatory foods. 

You can also start to ask yourself some of the questions that would help identify causes we’ve talked about here. For example, do you have a history of infection with Lyme disease or COVID? Has sleep been on the backburner during a busy time? Anything that you read here that gave you an “aha” moment is probably a good place to start. 

An Bioindividualized Approach to Chronic Pain 

In functional medicine, we treat every chronic pain case differently, because every individual case is different. Pain isn’t just one thing. The more we can address the individual and really understand what’s going on beneath the surface, the more effective a treatment approach will be. 

For bioindividualized support for your chronic pain, please feel free to book a consultation with our functional medicine telehealth team. We’d be happy to help. 

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. 

Photo: Unsplash.com

Sources

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• Goudman, L., Demuyser, T., Pilitsis, J. G., Billot, M., Roulaud, M., Rigoard, P., & Moens, M. (2024). Gut dysbiosis in patients with chronic pain: A systematic review and meta-analysis. Frontiers in Immunology, 15, 1342833.
• Minerbi, A., Gonzalez, E., Brereton, N. J., Anjarkouchian, A., Dewar, K., Fitzcharles, M. A., … & Shir, Y. (2019). Altered microbiome composition in individuals with fibromyalgia. Pain, 160(11), 2589-2602.
• Gigi, E. L., Rachmani, M., & Defrin, R. (2024). The relationship between traumatic exposure and pain perception in children: the moderating role of posttraumatic symptoms. Pain, 165(10), 2274-2281.
• Vadivelu, N., Kai, A. M., Kodumudi, G., Babayan, K., Fontes, M., & Burg, M. M. (2017). Pain and psychology—a reciprocal relationship. Ochsner Journal, 17(2), 173-180.
• Strath, L. J., Brooks, M. S., Sorge, R. E., & Judd, S. E. (2022). Relationship between diet and relative risk of pain in a cross-sectional analysis of the REGARDS longitudinal study. Pain Management, 12(2), 168-179.
• Cohen, S. P., Wang, E. J., Doshi, T. L., Vase, L., Cawcutt, K. A., & Tontisirin, N. (2022). Chronic pain and infection: mechanisms, causes, conditions, treatments, and controversies. BMJ medicine, 1(1), e000108.
• Ścieszka, J., Dąbek, J., & Cieślik, P. (2015). Post-Lyme disease syndrome. Reumatologia/Rheumatology, 53(1), 46-48.
• Batheja, S., Nields, J. A., Landa, A., & Fallon, B. A. (2013). Post-treatment lyme syndrome and central sensitization. The Journal of neuropsychiatry and clinical neurosciences, 25(3), 176-186.
• Tarleton, E. K., Kennedy, A. G., Rose, G. L., & Littenberg, B. (2020). Relationship between magnesium intake and chronic pain in US adults. Nutrients, 12(7), 2104.
• Goon, M., Schmidt, N., Berwal, D., Branisteanu, D. D., Barron, G., Morris, D. R., … & Pilitsis, J. G. (2025). Micronutrients and Chronic Pain: A Cross‐Sectional Analysis. Pain Practice, 25(5), e70053.
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