The Wahls Protocol: Nutrition for Autoimmune and Neurological Conditions

Origin: From Wheelchair to Bicycle

Dr. Terry Wahls is a clinical professor of internal medicine at the University of Iowa. In 2003, she was diagnosed with relapsing-remitting multiple sclerosis. By 2007, despite receiving the best conventional treatment available — including Tysabri and CellCept — her MS had progressed to secondary progressive. She was confined to a tilt-recline wheelchair, unable to sit upright without support.

Then she changed her approach. Drawing on evolutionary nutrition, functional medicine, and neuroscience research on mitochondrial function, she designed a nutrient-dense dietary protocol targeting the specific micronutrients her mitochondria, myelin, and neurotransmitters needed. The results were dramatic. Within a year she was walking without a cane. Within two years she completed an 18-mile bicycle ride. Her personal transformation has now been substantiated in clinical trials at the University of Iowa.

This protocol is not exclusive to MS. The principles apply to all autoimmune conditions, neurological diseases, and chronic inflammatory states. The Wahls Protocol is, at its core, a strategy for flooding the body with the raw materials it needs to repair itself.

The Three Levels

Wahls Diet (Level 1): Modified Paleo with a Micronutrient Target

The foundation is deceptively simple: eat 9 cups of vegetables and fruits every day, distributed across three specific categories.

Three cups of deeply colored fruits and vegetables: Berries (blueberries, blackberries, raspberries, strawberries), beets, carrots, red cabbage, sweet potatoes, cherries, pomegranate. These provide anthocyanins, carotenoids, polyphenols, and flavonoids — the antioxidant arsenal that protects mitochondria and neurons from oxidative damage.

Three cups of sulfur-rich vegetables: Broccoli, cauliflower, cabbage, Brussels sprouts, kale, onions, garlic, leeks, shallots, mushrooms, asparagus. Sulfur is the rate-limiting element in glutathione production — the body’s master antioxidant and primary detoxification molecule. Without adequate sulfur, Phase II liver detoxification stalls, glutathione drops, and oxidative stress accumulates.

Three cups of leafy greens: Kale, collards, Swiss chard, spinach, arugula, romaine, mustard greens, beet greens, dandelion greens. These provide magnesium (cofactor in 300+ enzymatic reactions), folate (methylation and DNA repair), vitamins K, A, and C, and chlorophyll (binds toxins in the gut).

Remove: Gluten, dairy, and eggs (the three most common immune triggers in autoimmune patients).

Add: Organ meats weekly, seaweed (iodine and trace minerals), fermented foods (sauerkraut, kimchi, kombucha), bone broth, quality fats (coconut oil, extra-virgin olive oil, animal fats from pastured sources).

Wahls Paleo (Level 2): Ancestral Nutrient Density

Everything from Level 1, intensified.

Organ meats become non-negotiable: A minimum of 12 ounces per week — liver, heart, kidney. This is nose-to-tail eating. Liver is the single most nutrient-dense food on Earth: the richest source of preformed vitamin A (retinol), vitamin B12 (up to 3,000% DV per 100g), folate, heme iron, copper, riboflavin, and CoQ10. Heart is the richest dietary source of CoQ10 — the electron carrier essential for mitochondrial ATP production. Kidney provides extraordinary concentrations of B12, selenium, and riboflavin.

Modern society abandoned organ meats in favor of muscle meat. This represents one of the most significant nutritional losses in human dietary history. Our ancestors prized organ meats above all other parts of the animal.

Seaweed daily: Kelp, nori, dulse, wakame. Rich in iodine (thyroid function), fucoidans (immune modulation), and a mineral profile that reflects ocean water — trace minerals that depleted soils no longer provide.

Fermented foods daily: Homemade sauerkraut, kimchi, water kefir, kombucha. Probiotic diversity from living fermented foods far exceeds what any capsule provides.

Raw foods daily: Raw vegetables for enzyme content and heat-sensitive nutrients.

Remove all grains (not just gluten-containing grains), all legumes, all white potatoes. Sweet potatoes are permitted in moderation. Reduce fruit to 1 cup daily.

Wahls Paleo Plus (Level 3): The Ketogenic Tier

All of Level 2 combined with ketogenic macronutrient ratios. This is the most therapeutically potent level.

Reduce non-starchy vegetables to 2-4 cups. Use coconut oil and MCT oil liberally. Protein stays at 6-12 ounces per day. Fat intake is high — enough to maintain nutritional ketosis (BHB 0.5-3.0 mmol/L).

This level is specifically designed for severe neurological conditions — progressive MS, Parkinson’s disease, traumatic brain injury, refractory autoimmunity. The ketogenic component provides alternative brain fuel (ketones) while the Wahls nutrient framework ensures mitochondrial and immune support.

Not everyone tolerates Level 3. Monitor adrenal function — cortisol can spike with aggressive carbohydrate restriction, particularly in patients with existing HPA axis dysregulation. If fatigue worsens or sleep deteriorates at Level 3, step back to Level 2 and stabilize.

Why Nine Cups Matters

Nine cups of vegetables and fruit is not arbitrary. It is the quantity required to provide micronutrient density that most modern diets catastrophically lack. The brain requires over 600 different micronutrients daily for optimal function — as cofactors for enzymatic reactions, building blocks for neurotransmitters, components of myelin, substrates for mitochondrial energy production.

The Standard American Diet provides a fraction of these requirements. Most Americans eat fewer than 2 servings of vegetables per day. The gap between what we eat and what our mitochondria need is the gap that chronic disease fills.

Nine cups specifically targets: B vitamins (mitochondrial electron transport chain cofactors), sulfur compounds (glutathione synthesis, detoxification), antioxidants (neuroprotection against free radical damage), minerals (enzyme cofactors for hundreds of metabolic reactions), and prebiotic fiber (microbiome nourishment).

The Evidence

Wahls’s 2014 pilot study enrolled MS patients on the Wahls Protocol combined with neuromuscular electrical stimulation and exercise. Results: significant reductions in fatigue (the most debilitating MS symptom), improved quality of life, and improved gait speed.

The 2019 randomized controlled trial at the University of Iowa compared the Wahls Protocol to the Swank diet (low saturated fat, recommended by the National MS Society). The Wahls Protocol produced significant improvements in the primary outcome — fatigue — along with improvements in walking speed and hand function in patients with progressive MS. Both diets outperformed usual care, but the Wahls Protocol showed advantages in several secondary measures.

Larger multicenter trials are ongoing. The evidence base continues to build, but the clinical outcomes in individual patients and the pilot/RCT data are already compelling.

Beyond MS: Applicable Conditions

The Wahls Protocol is not an MS diet. It is a mitochondrial and immune support diet. Any condition driven by mitochondrial dysfunction, inflammation, immune dysregulation, or nutrient depletion can benefit:

• Autoimmune diseases: Hashimoto’s thyroiditis, rheumatoid arthritis, lupus, Crohn’s disease, ulcerative colitis, psoriasis, celiac disease, Type 1 diabetes, Sjogren’s syndrome
• Neurological conditions: Parkinson’s disease, Alzheimer’s disease, traumatic brain injury, peripheral neuropathy, ALS (as supportive care)
• Chronic fatigue and fibromyalgia: Mitochondrial dysfunction is a central feature of both
• Mental health: Depression, anxiety, bipolar disorder — the gut-brain axis and neuroinflammation connect directly to mood disorders
• Metabolic syndrome: The nutrient density and elimination of processed food address insulin resistance, inflammation, and hepatic steatosis

Implementation: Making It Practical

Start at Level 1. Spend 4 to 12 weeks establishing the 9-cup habit and eliminating gluten, dairy, and eggs before advancing. This is already a dramatic shift for most people. Rushing to Level 3 creates overwhelm, die-off reactions, and dropout.

Batch cooking is essential. Roast large sheet pans of vegetables on Sunday. Make a week’s worth of bone broth. Cook a whole chicken and use every part. Prep containers of washed greens.

Soup is the easiest vehicle for 9 cups. A single large pot of soup can contain 4-6 cups of vegetables. Blend leafy greens into soups, smoothies, and sauces if chewing fatigue is an issue (common in neurological patients).

Organ meat strategies for the squeamish: Blend 2-4 ounces of raw liver into ground beef — the flavor disappears. Make pate with liver, butter, onions, and herbs. Use desiccated organ meat capsules (Ancestral Supplements, Heart & Soil) for those who genuinely cannot tolerate the taste. Heart can be sliced thin, marinated, and grilled — it tastes like steak.

Budget-friendly approaches: Frozen vegetables retain nearly all micronutrient content and cost a fraction of fresh. Whole chickens are far cheaper per pound than boneless breasts and provide bones for broth. Local farms and ethnic markets sell organ meats inexpensively because demand is low. Community-supported agriculture (CSA) boxes provide variety at lower cost.

How Wahls Differs from Standard Paleo and AIP

The Autoimmune Protocol (AIP) removes more foods than Wahls Level 1 — nightshades, nuts, seeds, eggs, and all potential immune triggers. But AIP does not prescribe specific quantities or categories of vegetables. A person could technically follow AIP eating 2 cups of vegetables daily and miss the micronutrient targets entirely.

Standard Paleo removes grains, legumes, dairy, and processed food. Excellent starting framework. But Paleo does not require 9 cups of vegetables, does not emphasize specific vegetable categories (deeply colored, sulfur-rich, leafy greens), and does not require organ meats.

The Wahls Protocol is distinguished by its insistence on nutrient quantity and specificity. Nine cups. Three categories. Organ meats. Seaweed. Fermented foods. This is not just about removing harmful foods — it is about aggressively providing the building blocks for repair. The removal piece clears the obstacles. The 9-cup framework supplies the materials. Both are necessary. Neither alone is sufficient.

For patients with autoimmune or neurological conditions who want the most evidence-based, nutrient-dense dietary framework available, the Wahls Protocol represents the current standard of care in functional medicine nutrition.