Migraines & Headaches: Finding the Root Cause

Migraine as Neurological Event

A migraine is not a headache that got promoted. It is a complex neurological event — a storm in the brain that unfolds in stages, driven by cortical spreading depression (a wave of neuronal depolarization that crawls across the cortex at 3mm per minute), trigeminal nerve activation, neurogenic inflammation, and massive release of calcitonin gene-related peptide (CGRP). The pharmaceutical industry spent billions developing CGRP-blocking drugs (the gepants and -umab monoclonal antibodies). Functional medicine asks a different question: why is CGRP being released in the first place?

The answer is never one thing. The migraine brain is a hypersensitive brain — a brain that responds to triggers that other brains shrug off. The job is to identify and remove the triggers, correct the underlying vulnerabilities, and raise the threshold so the storm never gathers.

The Four Phases of Migraine

Understanding the phases reveals the complexity:

Prodrome (24-48 hours before): Mood changes (irritability or euphoria), food cravings (especially sweets — the brain sensing energy deficit), excessive yawning, neck stiffness, frequent urination, constipation or diarrhea. This is the hypothalamus and brainstem activating. Most patients can learn to recognize their prodrome — it is an early warning system.

Aura (20-60 minutes): Only in 25-30% of migraineurs. Visual disturbances (scintillating scotoma — a shimmering arc of zigzag lines that expands across the visual field), numbness or tingling (usually face and hand — same side), speech difficulty, rarely motor weakness. This is cortical spreading depression — the wave of depolarization followed by suppression moving across the cortex.

Headache (4-72 hours): Throbbing, usually unilateral (but can be bilateral), moderate to severe. Nausea, vomiting, photophobia (light sensitivity), phonophobia (sound sensitivity), osmophobia (smell sensitivity). The trigeminal nerve is firing. Neurogenic inflammation makes blood vessels swell. Movement worsens it — the brain wants stillness and darkness.

Postdrome (24-48 hours after): The “migraine hangover.” Fatigue, cognitive fog, mood changes, neck soreness, food intolerance. The brain is recovering from the storm. This phase is often overlooked but significantly impacts quality of life.

Root Causes: The IFM Approach

The conventional approach gives everyone the same triptan and sends them home. The functional approach asks: what is YOUR driver?

Food Triggers

Not just “avoid chocolate.” The biochemistry matters:

• Tyramine: Found in aged cheese, red wine, cured meats, sauerkraut. Tyramine displaces norepinephrine from neurons, causing vasoconstriction followed by rebound vasodilation. People with low MAO-A enzyme activity are especially vulnerable.
• Histamine: Fermented foods, alcohol (especially red wine and beer), leftover food (bacterial histamine production increases with time), smoked fish, spinach, tomatoes, avocado, eggplant. Some migraineurs have diamine oxidase (DAO) deficiency — they cannot clear histamine efficiently.
• MSG (glutamate): Excitatory neurotransmitter that can overstimulate neurons in sensitive individuals.
• Aspartame: Phenylalanine and aspartic acid — excitotoxin potential.
• Nitrates: Hot dogs, bacon, deli meats — vasodilators.
• Gluten: In celiac disease and non-celiac gluten sensitivity, migraines resolve in essentially 100% of celiac patients who go strictly gluten-free (Gabrielli 2003). Even in NCGS, headache is the most common extra-intestinal symptom.
• Phenylethylamine: Chocolate, red wine — vasoactive amine.
• Sulfites: Wine (especially white), dried fruit, shrimp — trigger in sensitive individuals.

Hormonal Migraines

Estrogen withdrawal is the trigger — not high estrogen, but the drop. This explains why migraines cluster in the 2-3 days before menses (catamenial migraine) when estrogen plummets. Oral contraceptives with placebo weeks create artificial estrogen withdrawal. Perimenopause — with its chaotic hormonal fluctuations — is migraine hell for many women. After menopause, when estrogen stabilizes (at low levels), 70% of migraineurs improve.

Treatment: Magnesium glycinate 400mg/day (especially premenstrual), B6/P5P 50mg/day (supports progesterone and serotonin), vitex (chasteberry) 20-40mg/day (modulates prolactin and progesterone), bioidentical progesterone (GABA-A modulating metabolite allopregnanolone provides neuroprotection).

Magnesium Deficiency: The Universal Migraine Nutrient

This deserves its own section because it is that important. 50% of migraine patients are magnesium deficient when measured by RBC magnesium (serum magnesium is nearly useless — only 1% of body magnesium is in serum).

Magnesium blocks NMDA receptors (reducing excitotoxicity), inhibits cortical spreading depression (the wave that causes aura), relaxes vascular smooth muscle (reduces vasospasm), modulates serotonin receptors, and reduces substance P and CGRP release. It does everything a migraine drug tries to do.

Dose: 400-800mg magnesium glycinate or magnesium oxide daily. IV magnesium sulfate (1-2g) for acute attacks in emergency settings — works rapidly.

Mitochondrial Dysfunction

The brain is 2% of body weight but consumes 20% of the body’s energy. Migraine is, in part, a brain energy crisis. When mitochondria underperform, the brain’s threshold for triggering cortical spreading depression drops.

Three nutrients directly support mitochondrial electron transport:

• CoQ10: 200-400mg/day. Sandor 2005 RCT: 50% reduction in migraine attacks. CoQ10 shuttles electrons between Complex I/II and Complex III in the mitochondrial electron transport chain.
• Riboflavin (vitamin B2): 400mg/day. Schoenen 1998: number needed to treat (NNT) = 2.3. That means for every 2.3 patients treated, one gets significant benefit. For comparison, topiramate’s NNT is about 4. Riboflavin is better than most drugs, with essentially no side effects (just yellow urine).
• Alpha-lipoic acid: 600mg/day. Mitochondrial antioxidant, regenerates other antioxidants, crosses the blood-brain barrier.

Gut Connection

The gut-brain axis in migraine is robust:

• SIBO: Bacterial overgrowth produces excess gas, causes intestinal distension, triggers vagal afferents → brainstem nuclei → migraine. Treat the SIBO, reduce the migraines.
• H. pylori: Gasbarrini 1998 demonstrated that eradication of H. pylori significantly improved migraines in infected patients. The proposed mechanism: H. pylori-driven inflammation → increased gut permeability → systemic inflammation → neuroinflammation.
• Histamine intolerance: DAO deficiency → histamine accumulates → vasodilation, mast cell degranulation, neuroinflammation.
• Food sensitivities: IgG-mediated reactions drive chronic low-grade inflammation. Alpay 2010: IgG-based elimination diet reduced migraine days by 33-40%.

Other Root Causes

Cervicogenic: Upper cervical dysfunction (C1-C2), TMJ (temporomandibular joint) dysfunction, forward head posture (every inch of forward head posture adds 10 pounds of effective weight to the cervical spine). Physical therapy, chiropractic adjustment (especially upper cervical), dry needling of suboccipital muscles, trigger point release.

Toxins: Mold — headaches are a cardinal symptom of CIRS (Chronic Inflammatory Response Syndrome). Heavy metals — lead and mercury are both neurotoxic and can lower migraine threshold.

Autonomic dysfunction: Low vagal tone, sympathetic dominance, poor heart rate variability (HRV). Vagus nerve stimulation devices (gammaCore) are now FDA-approved for migraine.

The Prevention Protocol

Evidence-based, functional, and layered:

Foundation (everyone)

• Magnesium glycinate: 400-600mg/day. Non-negotiable. This is the single most important supplement for migraine prevention.
• Riboflavin (B2): 400mg/day. Strongest evidence of any supplement — NNT of 2.3.
• CoQ10: 200-400mg/day. Mitochondrial support.
• Omega-3: 2-3g/day EPA+DHA. Ramsden 2021 (NEJM): a high omega-3/low omega-6 diet reduced headache days by 30-40% and reduced headache severity. This was a landmark study in one of the most prestigious journals.
• Vitamin D: Target 50-70 ng/mL. Supplement 5000 IU/day if deficient.

Add Based on Profile

• Feverfew: 100-300mg/day standardized to parthenolide. Inhibits serotonin release from platelets, anti-inflammatory. Multiple positive trials. Takes 4-6 weeks for full effect.
• Butterbur (Petasites hybridus): 75mg 2x/day — MUST be PA-free (pyrrolizidine alkaloid-free) extract. Lipton 2004 RCT: 48% reduction in migraine frequency. PA-free extract (like Petadolex) is critical — non-PA-free butterbur is hepatotoxic.
• Ginger: 250mg at onset. Maghbooli 2014 RCT: ginger powder was as effective as sumatriptan for acute migraine, with fewer side effects. A rhizome competing with a pharmaceutical — and winning.
• Melatonin: 3mg at bedtime. Goncalves 2016: comparable to amitriptyline 25mg for migraine prevention, with far fewer side effects. Melatonin is anti-inflammatory, antioxidant, and regulates circadian rhythms (migraine brains have disrupted circadian biology).
• B6/P5P: 25-50mg/day. Especially important if histamine is a driver — P5P is the cofactor for diamine oxidase (DAO), the enzyme that degrades histamine.

For Acute Attacks

• Ginger 250mg (or fresh ginger tea)
• Magnesium (oral or IV)
• Peppermint essential oil topically to temples and neck (menthol activates TRPM8 receptors — analgesic and cooling)
• Dark, quiet room (reduce sensory input)
• Ice pack to back of neck (vagal stimulation + vasoconstriction)

The Elimination Diet Protocol

Remove the top food triggers for 4 full weeks: gluten, dairy, eggs, corn, soy, alcohol, caffeine, aged/fermented foods, artificial sweeteners, MSG, nitrates. Then reintroduce one food every 3-4 days, keeping a headache diary. This is laborious but reveals individual triggers with precision that no lab test can match.

Lifestyle: The Non-Negotiables

The migraine brain craves consistency. It is a brain that responds to change with electrical storms.

• Sleep: Regular schedule — same bedtime, same wake time, even on weekends. Both too little AND too much sleep trigger migraines.
• Meals: Regular meals at consistent times. Fasting triggers migraines through hypoglycemia and ketone shifts. Never skip breakfast.
• Hydration: Dehydration is one of the most common and most preventable migraine triggers. Half your body weight in ounces of filtered water daily.
• Exercise: 30 minutes of moderate aerobic exercise 3x/week. Varkey 2011: regular exercise was as effective as topiramate for migraine prevention. Exercise releases endorphins, improves mitochondrial function, reduces stress hormones, and modulates CGRP.
• Stress management: The migraine does not come during the stress — it comes during the let-down after the stress (“weekend migraine,” “vacation migraine”). This is the cortisol crash. Regular stress management practices (meditation, breathwork, yoga, progressive muscle relaxation) smooth the cortisol curve.
• Blue light: Reduce screen exposure in the evening. Blue light suppresses melatonin and triggers photosensitive migraine pathways. Blue-light-blocking glasses after sunset.

The migraine is a signal. The brain is saying: something is off. Fix the something, and the signal stops.