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A Functional Medicine Migraine Protocol: Comprehensive Testing, Nutritional Considerations, and Supplements

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A Functional Medicine Migraine Protocol: Comprehensive Testing, Nutritional Considerations, and Supplements

One billion people suffer from migraines around the world annually, affecting people of all ages. Migraines are ranked the second leading cause of disability worldwide and are consistently the fourth or fifth most common reason for emergency visits annually (16). If you or a loved one suffers from migraines, you can attest to how disabling migraines are. However, there is hope for migraine sufferers beyond conventional pharmaceutical options. Migraines respond very well to functional medicine's root-cause approach to treatment. By getting to the core of the problem, it is possible to achieve sustained relief and resolution of migraine headaches. This article will discuss functional medicine labs and natural modalities that can effectively prevent and treat migraines.


What is a Migraine?

According to the National Institute of Neurological Disorders and Stroke (NINDS), a migraine is "a type of headache characterized by recurrent attacks of moderate to severe throbbing and pulsating pain on one side of the head." Migraine pain is caused by the activation of nerve fibers within the wall of blood vessels traveling inside the brain's meninges (the three layers of membranes that line and enclose the brain and spinal cord). 

There are many types of migraines, the two most common being migraine with or without aura. Migraine with aura, previously called classic migraine, is characterized by visual, sensory, or language disturbances, known as auras, that precede or accompany the onset of a migraine headache. Migraine without aura, or common migraine, is the most common type of migraine that occurs without preceding neurological symptoms. 

Other types of migraine include (14, 21):  

  • Abdominal Migraine:  intense central abdominal pain associated with little-to-no headache and additional symptoms of nausea, vomiting, pallor, light sensitivity, and loss of appetite
  • Basilar-Type Migraine: Throbbing headache that is felt on both sides at the back of the head, most commonly in teenage girls. Additional symptoms include partial or total loss of vision or double vision, dizziness and loss of balance, poor muscle coordination, slurred speech, ringing in the ears, and fainting.
  • Hemiplegic Migraine: a rare and severe type of migraine that causes temporary paralysis on one side of the body before or during a headache. Vertigo, pricking or stabbing sensations, and difficulties seeing, speaking, or swallowing may begin prior to the headache.
  • Menstrual Migraine: a headache that affects women around the time of their period
  • Migraine without Headache: aura symptoms, nausea, and constipation without head pain
  • Ophthalmoplegic Migraine: an uncommon type of migraine associated with head pain, a droopy eyelid, large pupils, and double vision
  • Retinal Migraine: attacks of vision loss or disturbances in one eye associated with the onset of migraine
  • Status Migrainosus: a rare and severe migraine characterized by debilitating pain and nausea lasting at least 72 hours

Migraine Signs & Symptoms

Migraines are severe headaches that typically include a severe throbbing or pulsating headache, often on one side of the head, accompanied by sensitivity to light and sound, nausea, vomiting, and sometimes visual disturbances or auras. Untreated migraines usually last 4-72 hours, and patients are generally asymptomatic between attacks. (14

Four phases of a migraine attack have been identified. Not all migraine sufferers experience all four phases, and the duration and severity of each stage can vary from person to person. (16

  1. Prodrome: can occur hours or even days before the actual headache and is characterized by subtle changes in mood, energy levels, or appetite. This phase may involve irritability, fatigue, food cravings, or heightened sensitivity to light or sound.
  2. Aura: occurs in 25% of migraine sufferers and is characterized by transient neurological symptoms such as visual disturbances (flashing lights, blind spots), sensory changes (tingling, numbness), or even difficulty speaking. The aura lasts no longer than an hour and is a warning sign of an impending headache. 
  3. Headache: may last anywhere from a few hours to a few days and is often accompanied by nausea, vomiting, and increased sensitivity to light and sound.
  4. Postdrome: the headache gradually subsides, but individuals may feel exhausted, mentally foggy, or experience lingering symptoms such as mild headache, sensitivity, or mood changes. 

What Causes Migraines?

The exact cause of migraines is still not fully understood, but they are believed to result from a complex interplay of genetic, environmental, and neurological factors. One widely accepted theory is that migraines are initiated by abnormal brain activity that affects the blood vessels and chemicals in the brain. Changes in blood flow and the release of certain neurotransmitters, such as serotonin, play a role in migraine development. (13

Furthermore, the central nervous system is believed to be involved in migraines. Certain brain regions are thought to become overly sensitive or reactive, leading to a cascade of events resulting in the symptoms of migraines. The trigeminal nerve, a major pain pathway, is also believed to play a role in transmitting pain signals during a migraine. (16

Migraine has a strong genetic component. Migraines tend to run in families; people with a family history of migraines are three times more likely to experience them. Specific genes related to regulating blood vessels and neurotransmitters have also been associated with migraines. (16

Many triggers can contribute to migraine episodes. These triggers vary among individuals but can include hormonal changes, such as fluctuations in estrogen levels, certain foods and beverages (e.g., aged cheese, chocolate, alcohol), stress, lack of sleep, bright lights, strong odors, and changes in weather or barometric pressure. (7, 21)  

Functional Medicine Labs to Test for Root Cause of Migraines

Migraines can be diagnosed clinically using the ICHD-3 Diagnostic Criteria for Migraine. However, after making a clinical diagnosis, functional medicine doctors generally order specialty tests to holistically grasp a patient's migraine root causes and triggers to create holistic, customized prophylactic treatment plans.

Comprehensive Hormone Panel

About three out of four people with migraines are women; this increased female prevalence is thought to be attributed to monthly hormonal shifts related to the menstrual cycle. The sudden drop in estrogen and progesterone that occurs before a period is believed to trigger a migraine. Irregular hormonal imbalances at other points in the menstrual cycle can also contribute to increased migraine frequency. Therefore, mapping the natural levels of estrogen and progesterone with a hormone panel throughout a woman's menstrual cycle can be highly beneficial in evaluating the role of sex hormones as a cause of migraine. (12

Sleep and Stress Panel

Other hormones that control our circadian rhythm and stress response can influence how we sleep and perceive stress. Melatonin and cortisol are the primary hormones involved in the sleep-wake cycle. In addition, cortisol is one of the primary hormones produced by the body as part of the natural stress response. A salivary test can measure cortisol and melatonin throughout the day to qualify and quantify the body's secretion curve for each hormone. 

Food Sensitivity 

Several dietary triggers are well documented to prompt the onset of migraine, including alcohol and nitrate- and tyramine-rich foods. However, substantial evidence suggests that IgG immune reactivity to various foods is linked to migraines. For example, this study confirmed that individuals who regularly experience migraines are more likely to test positive for more IgG food sensitivities than those who don't experience migraines regularly. That study, in addition to this one, has also concluded that therapeutic elimination of IgG-reactive foods resulted in the successful control and reduction of migraine headaches without needing medications. A food sensitivity panel can help identify food sensitivities to make dietary interventions and modifications more effective for patients. 

Micronutrient Analysis

Deficiencies in magnesium, niacin, riboflavin, cobalamin, CoQ10, carnitine, alpha-lipoic acid, and vitamin D have been associated with migraine (7). Nutrient testing allows for identifying nutrient insufficiencies and deficiencies to create a personalized supplementation plan to restore optimal nutrient status. 


Conventional Treatment for Migraines

Drug therapy for migraine is divided into acute "abortive" and preventive treatment. Abortive medications are taken as soon as symptoms occur to relieve pain and include triptan drugs, ergot-derivative drugs, over-the-counter analgesics (such as ibuprofen or acetaminophen), and antiemetics. Preventive medications are taken regularly to prevent and reduce the severity of future migraine attacks. First-line preventive medications include divalproex, topiramate, metoprolol, propranolol, and timolol. 

Functional Medicine Treatment Protocol for Migraines

Depending on the frequency and severity of migraines, a functional medicine doctor may recommend some combination of the above medications to prevent and treat migraines. However, a functional medicine treatment protocol also incorporates other modalities that address the underlying causes and triggers of migraines identified with specialty testing. 

Therapeutic Diet and Nutrition Considerations for Migraines

Dietary intervention is a powerful tool in the treatment of migraines, and numerous studies have found elimination diets of various sorts to reduce migraine severity and frequency. Elimination diets can be created based on the common migraine food triggers, customized based on food sensitivity test results, or a combination of the two. For the highest chance of success, patients should follow an elimination diet for 4-12 weeks before reintroducing foods back into the diet to help identify dietary triggers. (9)

Some of the most commonly reported triggers for migraine include chocolate, cheese, nuts, citrus fruits, processed meats, monosodium glutamate (MSG), aspartame, fatty foods, coffee, and alcohol (9). This handout offers a user-friendly table that lists general recommendations for a generalized migraine prevention diet. It can be an excellent starting point for patients who have yet to experiment with making any dietary changes for migraine treatment. 

Fasting, missing meals, and overeating are common triggers for migraine (9). Given this, patients should be instructed to eat at regular time intervals. 

Supplements Protocol for Migraines

A number of natural herbs and supplements have been reported effective in treating and preventing migraine headaches. While the protocol below doesn't include supplemental options for balancing hormones, these should be considered along with healthy lifestyle habits if indicated per the patient's lab results.


Magnesium helps to maintain vascular tone and prevent neuronal excitability. Low brain and tissue concentrations of magnesium have been found in patients with migraine. Citrate and oxide magnesium forms are most commonly used in clinical studies; magnesium supplementation is linked to reduced intensity or frequency of migraine attacks and improved cerebral blood flow (26). (25

Dose: 600 mg daily

Duration: 6-12 weeks


Feverfew (Tanacetum parthenium) is an herb native to southeastern Europe. Researchers believe feverfew's parthenolide constituent has anti-inflammatory effects and relieves smooth muscle spasms, making it effective against migraines. (5

A 1983 survey found that 70% of 270 migraine sufferers who had eaten 2-3 fresh feverfew leaves daily had decreased frequency and intensity of their migraines (5). Other studies that have used feverfew in combination with other botanicals and natural substances have also shown a reduction in the frequency and severity of migraines (11, 20).  

Dose: 25-100 mg dried leaves twice daily or 0.25-0.5 mg parthenolide twice daily

Duration: at least three months


Butterbur (Petasites hybridus) root can be used to prevent migraines. Studies report 50-68% reductions in migraine frequency with butterbur root extract supplementation. The plant contains liver-toxic pyrrolizidine alkaloids, so make sure to use alkaloid-free extract preparations for safe supplementation. (26)

Dose: 50-100 mg twice daily with meals

Duration: 4-6 months, then taper dose until migraine frequency begins to increase to determine maintenance dose

Vitamin B2 (Riboflavin)

Low vitamin B2 status can lead to mitochondrial dysfunction, leading to the development of migraines. A systematic review concluded that riboflavin supplementation is safe and effective for preventing migraine symptoms in adults. Additionally, this study found that riboflavin dosed at 400 mg daily could reduce the usage of abortive migraine medications after 3-6 months of treatment. 

Dose: 400 mg daily

Duration: at least three months


Similarly to riboflavin, CoQ10 supports mitochondrial function and energy metabolism. Studies support using CoQ10 in 100-300 mg daily doses as a safe and effective intervention for reducing migraine headaches' frequency, duration, and severity (18, 19).  

Dose: 100 mg 1-3 times daily 

Duration: at least three months

When to Retest Labs

Research indicates that complementary and integrative modalities, including dietary modifications and natural supplementation, require up to three months to have maximum effect in patients. Retesting hormonal and micronutrient panels is appropriate for monitoring patient response to intervention and guiding treatment plan modifications. 

Learning More About Migraines



There are many types of migraines, all of which are extremely painful and disabling. While conventional medicine uses various medications to acutely treat and prevent migraines, a functional and integrative medicine approach uses additional tools to correct underlying imbalances related to hormones, food sensitivities, and nutrient deficiencies that are known to contribute to the frequency and severity of migraines. Doctors can use the sample protocol outlined in this article to help patients achieve better long-term control and complete resolution of their migraines.

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.
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Lab Tests in This Article


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