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A Functional Medicine Fibromyalgia Protocol: Lab Testing, Therapeutic Diet, and Supplements

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A Functional Medicine Fibromyalgia Protocol: Lab Testing, Therapeutic Diet, and Supplements

The CDC estimates four million American adults (2% of the adult population) are afflicted with fibromyalgia. Fibromyalgia can cause varying degrees of disability, ranging from mild to severe, depending on the individual. Many individuals with fibromyalgia experience limitations in their ability to perform regular activities, work, engage in social interactions, and maintain overall well-being. Conventional approaches to fibromyalgia treatment often focus on symptom management, which may not address the underlying root causes. This is where a functional medicine approach becomes crucial. By addressing the individual's unique factors, functional medicine recognizes the complex nature of fibromyalgia and offers a framework to identify and treat the root causes of this challenging condition.


What is Fibromyalgia?

Fibromyalgia is a chronic and complex rheumatologic disorder affecting millions worldwide. It is characterized by widespread musculoskeletal pain, fatigue, and tenderness in specific areas of the body. Fibromyalgia can be understood as a neurosensory disorder that affects the central nervous system's processing of pain signals. The brain's perception and interpretation of pain signals are altered in individuals with fibromyalgia, leading to an amplified pain response even to stimuli that are not typically perceived as painful. This heightened sensitivity is referred to as central sensitization. Along with pain, fibromyalgia can involve other neurosensory symptoms, such as heightened sensitivity to touch, temperature, and sound. Fatigue, sleep disturbances, and cognitive difficulties are also common in individuals with fibromyalgia, further highlighting the involvement of the central nervous system. (8, 15)

Fibromyalgia Signs & Symptoms

The cardinal symptom of fibromyalgia is bilateral musculoskeletal pain, which involves the upper and lower parts of the body and is present for at least three months. The pain is classically described as a dull muscle ache, but patients may also complain of joint pain. Commonly affected areas include the neck, shoulders, chest, hips, knees, and elbows, where specific tender points can be found. (1

The other hallmark symptom of fibromyalgia is persistent, chronic fatigue, even after getting enough sleep. The fatigue often interferes with daily activities. Minor activities may aggravate the pain and fatigue, although prolonged inactivity can also increase symptoms. Sleep disturbances are common; patients may complain of being light sleepers with frequent wakings in the early morning. (1

Often called "fibro fog," patients experience cognitive disturbances, such as difficulty paying attention, brain fog, trouble doing tasks requiring rapid thought changes, and poor memory. (1

Individuals with fibromyalgia may also experience a range of secondary symptoms, such as (1): 

  • Anxiety and/or depression
  • Headaches: migraines and tension headaches
  • Irritable bowel syndrome (IBS)
  • Gastroesophageal reflux disease (GERD)
  • Dry eyes
  • Shortness of breath
  • Heart palpitations

What Causes Fibromyalgia?

While the exact cause of fibromyalgia remains elusive, researchers believe it arises from genetic, environmental, and physiological factors. Several key factors have been identified that contribute to the development of fibromyalgia.

One primary factor is believed to be abnormal pain processing in the central nervous system. Individuals with fibromyalgia have heightened sensitivity to pain due to changes in how their brain and spinal cord process pain signals. This altered pain processing can amplify pain sensations, leading to widespread and chronic pain throughout the body. Researchers have noted imbalances in neurotransmitters, including glutamate, substance P, serotonin, norepinephrine, and dopamine, further supporting this theory. (1

Genetics may also play a role in fibromyalgia. Although specific genes have not been identified, studies have shown a familial tendency for fibromyalgia, suggesting a genetic component.

Environmental factors such as physical or emotional trauma, infections, or stressful life events can trigger or exacerbate fibromyalgia symptoms. These triggers may cause nervous system changes and lead to fibromyalgia onset in susceptible individuals. (1)

Functional Medicine Labs to Test for Root Cause of Fibromyalgia

Fibromyalgia can be challenging to diagnose as no specific laboratory tests or imaging studies confirm it. Diagnosis is usually based on the presence of widespread pain and the exclusion of other conditions that could account for the symptoms.

Routine Blood Work

A standard lab panel including a CBC, CMP, thyroid hormones, ESR, CRP, and ANA should be included in the initial diagnostic evaluation for patients with fibromyalgia to rule out other conditions that could account for the symptoms. This panel includes lab markers that can screen for infection, anemia, electrolyte imbalances, liver/kidney disease, dysglycemia, thyroid dysfunction, autoimmune disease, and quantify systemic inflammation. 

Organic Acids

An organic acids test (OAT) is a comprehensive diagnostic tool that assesses various metabolic markers through the analysis of organic acids present in urine. This test provides valuable insights into several aspects of health, including nutrient deficiencies, oxidative stress, detoxification capacity, neurotransmitter function, and microbial overgrowth. Functional medicine practitioners can identify imbalances and dysfunctions within the body's metabolic processes by analyzing these organic acids. This information may indicate the need for additional testing and can guide personalized treatment plans, including targeted nutritional interventions, lifestyle modifications, and supplementation, to address fibromyalgia's underlying causes. 

Infectious Panel

The role of viral and bacterial infections in causing fibromyalgia is a subject of ongoing research. While it is clear that fibromyalgia can be triggered or exacerbated by infections, the exact mechanisms linking the two are not yet fully understood. Studies have suggested that viral and bacterial infections, including Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), hepatitis C, HIV, and Lyme disease, trigger an abnormal immune response that triggers persistent inflammation. Ordering an infectious panel to screen for immune activation against various infectious agents can screen for chronic infections contributing to fibromyalgia development and symptom severity. (4

Comprehensive Gut Assessment

Increasing research suggests that the gut microbiome, the diverse community of microorganisms residing in the gastrointestinal tract, may play a role in the development and symptoms of rheumatic conditions. The gut microbiome profoundly influences immune function, neurotransmitter production, and the gut-brain axis, all of which can impact fibromyalgia. Furthermore, studies have shown fibromyalgia patients to have increased rates of dysbiosis, small intestinal permeability, and small intestinal bacterial overgrowth (SIBO) compared to healthy controls (15). 

Therefore, a comprehensive gut assessment utilizing a combination of specialty tests, including a comprehensive stool analysis, SIBO breath test, and intestinal permeability screen, can screen for these distinct patterns and shifts in gut health and function related to fibromyalgia.

Nutritional Assessment

Multiple nutrient deficiencies have been associated with fibromyalgia, including vitamins B12 and D, magnesium, calcium, and omega-3 fatty acids (8). A micronutrient test measures the levels of these, among many other essential nutrients.


Fibromyalgia is more common in women, partially attributed to the hormonal effects of the menstrual cycle on central nervous system functioning (1). Additionally, patients with fibromyalgia have been found to have abnormal hypothalamic-pituitary-adrenal (HPA) stress responses. A DUTCH test measures both reproductive and adrenal hormones to assess for imbalances in the endocrine pathways related to ovarian and adrenal function.


Conventional Treatment for Fibromyalgia

Management of fibromyalgia involves a multimodal approach that includes medication, physical therapy, exercise, stress reduction techniques, and lifestyle modifications. The primary focus is managing pain, improving sleep, addressing psychological well-being, and promoting overall physical function. Nonsteroidal anti-inflammatory drugs (NSAIDs) and analgesics may be prescribed to help manage pain, although their effectiveness in fibromyalgia is limited. Antidepressants, particularly selective serotonin reuptake inhibitors (SSRIs) and serotonin-norepinephrine reuptake inhibitors (SNRIs), are commonly prescribed to help modulate pain perception, improve sleep, and manage associated depression or anxiety. Muscle-relaxant or anticonvulsant medications may also be considered for symptom management. Additionally, non-pharmacological interventions, including physical therapy, exercise programs, cognitive-behavioral therapy (CBT), and stress reduction techniques, are often recommended to improve physical function, reduce pain, and address the emotional impact of fibromyalgia. Treatment plans are typically tailored to the individual's specific symptoms and may involve a combination of these approaches to achieve optimal symptom control and enhance overall well-being. (5

Functional Medicine Treatment Protocol for Fibromyalgia

A functional medicine approach to treating fibromyalgia focuses on personalized and patient-centered care, aiming to identify and address the underlying root causes of the condition. Practitioners create a tailored treatment plan by assessing an individual's medical history, lifestyle factors, genetics, and environmental exposures. They prioritize addressing the root causes, such as nutritional imbalances, hormonal dysregulation, gut health issues, chronic infections, toxins, and psychological stress. This systems-based approach recognizes the interconnectedness of various body systems and aims to restore balance and optimize overall wellness. Lifestyle modifications, nutritional support, and collaborative patient empowerment are key components, encouraging active participation in the healing process to improve long-term health and vitality. 

In addition to the nutritional considerations and supplements discussed in detail below, providers should help patients establish a solid basis for optimal health by advising on the importance of exercise and physical medicine, stress management, sleep, and counseling for trauma. Other complementary and integrative modalities that can be integrated into a holistic treatment plan include chiropractic, massage therapy, acupuncture, and infrared light therapy.

Therapeutic Diet and Nutrition Considerations for Fibromyalgia

A 2019 systematic review revealed that specific diets have shown promise in alleviating pain and enhancing the quality of life for individuals with fibromyalgia. Among the diets investigated, the hypocaloric (low-calorie) diet, the low-FODMAP diet, and the raw vegetarian diet demonstrated positive outcomes. These diets were associated with reduced inflammation markers, improved sleep quality, and decreased levels of anxiety and depression, as observed in the review. 

Likely, these diets demonstrate positive health outcomes given their anti-inflammatory natures. By reducing ultra-processed foods and incorporating whole foods rich in antioxidants, omega-3 fatty acids, and phytonutrients, any nutrient-dense, anti-inflammatory diet can help minimize inflammation, support optimal nutrition, improve gut microbiome balance, stabilize weight and energy levels, and positively impact mood, cognitive function, sleep quality, and stress resilience. These factors contribute to a potential reduction in fibromyalgia symptoms and improved quality of life.

Supplements Protocol for Fibromyalgia

Supplements can be used with or as natural alternatives to pharmaceutical medications to correct imbalances identified on testing and improve symptoms related to fibromyalgia. Below is a sample protocol that doctors can use in clinical practice.


A high-potency multivitamin can provide general nutritional support to treat and prevent nutritional deficiencies associated with fibromyalgia. A multivitamin can support energy production, immune function, and neurotransmitter synthesis.

Dose: Per label instructions 

Duration: Ongoing


5-Hyroxytryptophan (5-HTP) is an amino acid precursor for the neurotransmitter serotonin. Low serotonin levels are associated with fibromyalgia pain, depression, and sleep disturbances. A 90-day clinical trial demonstrated that 5-HTP improved pain intensity, the number of tender points, sleep, fatigue, anxiety, and overall quality of life in patients with fibromyalgia.

Dose: 50-100 mg daily

Duration: 3 months

Magnesium Malate

Magnesium is often supplemented alongside a multivitamin to improve ATP production in skeletal muscle and decrease muscle tone and spasms. Studies show that patients with fibromyalgia tend to have lower blood levels of magnesium compared to healthy controls, and supplementation improves fatigue, sleep, mood, muscle pain, and tender points. 

Dose: 300 mg 2-3 times daily

Duration: 3 months

Fish Oil

Fish oil is rich in omega-3 fatty acids, which are anti-inflammatory and important for brain function. Numerous studies have shown omega-3 fatty acids' ability to reduce biochemical markers of inflammation, reduce joint pain intensity, reduce migraine frequency and severity, improve depression scores, and enhance cognitive function. 

Dose: 1,000-2,000 mg of combined EPA + DHA daily

Duration: at least 3-6 months

When to Retest Labs

The decision to retest should be determined by clinical necessity, the patient's response to treatment, and patient/doctor preference. Functional medicine labs are typically reordered between 3-12 months after baseline to assess patient progress; however, in some cases, clinical necessity will dictate labs be reordered sooner than this to monitor the patient's health. 

Learning More About Fibromyalgia



Fibromyalgia is a complex pain condition that significantly impacts the affected individual's quality of life and ability to function. A functional medicine approach offers alternative tools and resources to target and correct the underlying causes of disease. A multimodal, holistic treatment plan improves symptom and function scores and allows patients to regain the freedom to enjoy life.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
Learn More

Lab Tests in This Article

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