The 21-Day Functional Medicine Detox Program

Why Three Weeks

Twenty-one days is not arbitrary. It takes roughly 72 hours for caffeine withdrawal to peak and resolve. It takes 5-7 days for blood sugar patterns to stabilize after removing refined carbohydrates. It takes 14-21 days for IgG-mediated food sensitivities to clear the system. It takes 2-3 weeks for the gut lining to begin measurable repair. And it takes approximately 21 days to establish a new habit pattern — not perfected, but initiated.

This program is not a juice cleanse, a starvation diet, or a punishment. It is a structured physiological reset based on the IFM (Institute for Functional Medicine) framework: reduce the toxic burden, support the body’s innate detoxification pathways, heal the gut, identify reactive foods, and build a sustainable anti-inflammatory foundation.

Before You Begin: The Medical Symptom Questionnaire (MSQ)

Score your symptoms before starting. The MSQ rates symptoms across 15 categories (head, eyes, ears, nose, mouth/throat, skin, heart, lungs, digestive, joints/muscles, weight, energy, mind, emotions, other) on a 0-4 scale. Total score gives you a baseline. Re-score on day 21.

Typical results: a starting score of 40-80 drops to 10-30. Some patients drop 60-70%. The number itself matters less than the direction — it makes the invisible visible. Symptoms you have normalized for years (chronic congestion, brain fog, joint stiffness, afternoon fatigue, poor sleep) often resolve, and you did not even know they were treatable because you thought they were just “how you are.”

Who Should NOT Do This Program

• Pregnant or breastfeeding: Mobilizing stored toxins could expose the fetus or nursing infant. Detoxification programs should be done before conception or after weaning
• Active eating disorder (without professional supervision): Structured elimination can trigger restrictive patterns. Only proceed with a therapist actively involved
• Severely malnourished or underweight: The priority is nutritional repletion, not elimination
• Active cancer treatment: Detoxification may interfere with chemotherapy pharmacokinetics. Discuss with oncologist
• Type 1 diabetes or brittle Type 2: Major dietary changes require medication adjustment; work with your prescribing physician throughout
• Medications with narrow therapeutic index: Warfarin, lithium, anti-seizure medications — detoxification can alter drug metabolism. Physician supervision required

Phase 1: Prepare & Remove (Days 1-7)

This is the hardest week. The body is withdrawing from stimulants, sugar, and inflammatory triggers. Expect it. Plan for it.

What Comes Out

Remove completely for 21 days:

• Gluten: All wheat, barley, rye, spelt, kamut, and anything derived from them. Read labels — gluten hides in sauces, dressings, supplements, and processed foods
• Dairy: All cow’s milk products (milk, cheese, yogurt, butter, whey, casein). Ghee is usually tolerated (casein removed). Goat/sheep dairy removed for strictest protocols
• Sugar and artificial sweeteners: Refined sugar, high-fructose corn syrup, agave, aspartame, sucralose, saccharin. Small amounts of raw honey, maple syrup, or stevia are acceptable
• Alcohol: Complete elimination. No exceptions
• Caffeine: Taper over 3-4 days (cold turkey produces brutal headaches). Day 1: half your usual amount. Day 2: quarter. Day 3: green tea only. Day 4: herbal tea only
• Corn, soy, eggs: Common reactive foods. Remove for the full 21 days
• Processed foods: Anything with ingredients you cannot pronounce or would not find in a kitchen
• Industrial seed oils: Canola, soybean, corn, cottonseed, sunflower, safflower. Replace with olive oil, avocado oil, coconut oil

What Goes In

• Vegetables: 6-8 cups daily (measured raw, roughly 3-4 cups cooked). Emphasis on cruciferous (broccoli, cauliflower, Brussels sprouts, kale, cabbage — Phase I and Phase II liver detox support), dark leafy greens, alliums (onion, garlic — sulfur for glutathione), and colorful variety
• Clean protein: Wild-caught fish, pasture-raised poultry, grass-fed meat, legumes (lentils, chickpeas, black beans — unless GI distress), hemp seeds, pumpkin seeds
• Healthy fats: Extra virgin olive oil, avocado, coconut oil, nuts (except peanuts), seeds, olives
• Gluten-free whole grains (optional): Quinoa, rice, millet, buckwheat, amaranth — small portions
• Fruit: Limited to 1-2 servings daily. Berries preferred (lower glycemic, highest polyphenol)
• Water: 8+ glasses daily. Half your body weight in ounces is a rough guide. Filtered (ideally reverse osmosis or carbon block to remove chlorine, fluoride, heavy metals, pharmaceuticals)

Daily Practices (Begin Day 1)

• Morning: glass of warm water with lemon juice (stimulates bile flow and digestive enzyme production)
• Movement: 30 minutes daily — walking, yoga, swimming, cycling. Nothing extreme (intense exercise increases cortisol and may overwhelm detox capacity)
• Sleep: 8+ hours. This is when Phase I and Phase II liver detoxification are most active. Prioritize sleep above exercise if you must choose
• Journal: Track symptoms, energy, mood, digestion, sleep quality daily. You will want this record

Core Supplement Stack (Start Day 1)

Supplement	Dose	Timing	Purpose
Multivitamin (methylated B’s)	Per label	Morning with food	Nutritional foundation, methylation support
Omega-3 (EPA/DHA)	2g combined	With food	Anti-inflammatory
Magnesium glycinate	400mg	Bedtime	Relaxation, bowel motility, hundreds of enzymatic reactions
Probiotics (multi-strain)	20-50 billion CFU	Morning, empty stomach	Gut microbiome support
Fiber (ground flaxseed)	2 tablespoons	In smoothie or water	Binds toxins in GI tract, estrogen metabolism
Vitamin D3	2000-5000 IU	Morning with fat	Immune modulation, detox enzyme support

Withdrawal Symptoms (Days 2-5)

Expect some or all of: headache (caffeine, sugar), fatigue (your body is redirecting energy to detoxification), irritability (blood sugar adjustment, neurotransmitter shifts), brain fog, muscle aches, skin breakouts (toxins mobilizing through skin), intensified body odor or stool changes, vivid dreams, cravings.

Management: hydrate aggressively (water, herbal tea, bone broth), rest, take Epsom salt baths (magnesium sulfate supports detoxification and relaxation), go to bed early, know this is temporary. Most withdrawal peaks at days 3-4 and resolves by day 7.

Phase 2: Deep Cleanse (Days 8-14)

Withdrawal is largely past. Energy often begins to improve, sometimes dramatically. This is the week to intensify detoxification support.

Liver Support

The liver runs detoxification in two phases. Phase I (cytochrome P450 enzymes) converts fat-soluble toxins into intermediate metabolites — which are often MORE reactive and toxic than the original compounds. Phase II (conjugation pathways — glucuronidation, sulfation, glutathione conjugation, acetylation, methylation, amino acid conjugation) attaches molecules to these intermediates to make them water-soluble for excretion via bile (stool) or kidneys (urine).

If Phase I runs fast but Phase II is sluggish — as happens with genetic polymorphisms, nutrient deficiencies, or toxic overload — intermediary metabolites accumulate and cause damage. This is the most common pattern in environmental illness.

Add during week 2:

Supplement	Dose	Target
Milk thistle (silymarin)	200-400mg	Hepatoprotective, glutathione support, Phase I/II
NAC (N-acetylcysteine)	600mg 2x daily	Glutathione precursor (the body’s master detoxifier)
Dandelion root	500mg or as tea	Choleretic (stimulates bile flow)
Artichoke extract	500mg	Choleretic, hepatoprotective
Calcium-D-glucarate	500mg	Supports glucuronidation pathway, estrogen clearance
Sulforaphane (broccoli sprout extract)	30-50mg	Activates Nrf2, upregulates Phase II enzymes
Turmeric/curcumin	500-1000mg	Anti-inflammatory, Phase II support

Enhanced Elimination Practices

• Dry skin brushing: Before showering, brush skin with natural bristle brush in long strokes toward the heart. Stimulates lymphatic drainage, exfoliates dead skin, opens pores. 3-5 minutes
• Sauna/sweating: 2-3 sessions this week, 15-30 minutes each. Infrared sauna preferred (lower temperature, deeper tissue penetration). If no sauna access: hot Epsom salt baths (2 cups Epsom salt, 20 minutes), exercise to sweating
• Castor oil packs: Cold-pressed castor oil on flannel, placed over the liver (right upper abdomen under ribcage), covered with plastic wrap, heated with hot water bottle, 30-60 minutes. Stimulates liver circulation, lymphatic drainage, and relaxation. 3-4 evenings this week
• Fiber: Increase ground flaxseed to 2-3 tablespoons daily. Add psyllium husk 1 teaspoon in water if needed. Toxins are excreted through bile into stool — without adequate fiber, they are reabsorbed (enterohepatic recirculation)
• Green smoothie: Daily blended greens (spinach, kale, parsley, cilantro, cucumber) + berries + ground flaxseed + protein powder + water or coconut water. This is the most nutrient-dense meal of the day

Optional: Binders

Binders are substances that trap toxins in the GI tract and prevent reabsorption. Take between meals (at least 1 hour before or 2 hours after food and supplements — binders are not selective, they bind nutrients too).

• Activated charcoal 500-1000mg between meals
• Bentonite clay 1 teaspoon in water
• Modified citrus pectin 5-15g
• Chlorella 2-3g (also provides chlorophyll and B12)

Use binders especially if experiencing die-off or detox reactions (headache, fatigue, skin symptoms that worsen before improving).

Phase 3: Restore & Reintroduce (Days 15-21)

Gut Healing Intensification

The elimination diet has removed inflammatory triggers. Now actively repair the gut lining:

Supplement	Dose	Mechanism
L-Glutamine	5g 2x daily	Primary fuel for enterocytes, tight junction repair
Zinc carnosine	75mg 2x daily	Mucosal healing, antimicrobial
Bone broth	1-2 cups daily	Collagen, glycine, glutamine, minerals
Probiotics (increase)	50-100 billion CFU	Repopulate beneficial species
Deglycyrrhizinated licorice (DGL)	400mg before meals	Mucosal protection, soothing
Aloe vera juice	2-4 oz	Anti-inflammatory, mucosal healing

Strategic Reintroduction (Begins Day 19)

This is the most clinically valuable part of the program — it turns your body into a diagnostic instrument.

Rules:

1. Reintroduce one food at a time
2. Eat a generous portion of the test food 2-3 times on the test day
3. Monitor for 72 hours before introducing the next food
4. Track: energy, mood, sleep, digestion (bloating, gas, bowel changes), joint pain, skin changes, headaches, brain fog, nasal congestion, heart rate
5. If a reaction occurs, that food is a current sensitivity. Remove it again and wait until symptoms clear before testing the next food

Recommended reintroduction order (most common triggers first):

• Day 19: Gluten (pure wheat bread or pasta — not mixed with other triggers)
• Day 22: Dairy (plain yogurt or milk — single source)
• Day 25: Eggs (whole, cooked simply)
• Day 28: Corn
• Day 31: Soy

If you react to a food: it does not necessarily mean lifelong avoidance. It means current sensitivity — often driven by gut permeability and immune reactivity that can heal over 3-6 months of gut repair. Retest in 3 months.

End-of-Program Assessment

• Re-score the Medical Symptom Questionnaire
• Compare with baseline
• Note which symptoms resolved, improved, or persisted
• Note energy level, sleep quality, mental clarity, digestive function, skin appearance
• Identify your reactive foods
• Build your maintenance plan

Meal Ideas

Green Smoothie (Daily Foundation)

2 cups spinach or kale, 1 cup frozen berries, 1 tablespoon ground flaxseed, 1 scoop plant-based protein powder (pea or hemp), 1 tablespoon almond butter, 1 cup water or coconut water. Blend until smooth.

Elimination-Diet-Safe Meals

• Baked wild salmon with roasted broccoli and sweet potato
• Turkey lettuce wraps with avocado, shredded carrot, cucumber, tahini dressing
• Lentil soup with turmeric, ginger, garlic, greens
• Cauliflower rice stir-fry with chicken, vegetables, coconut aminos (soy-free), ginger
• Bone broth with shredded chicken, zucchini noodles, mushrooms
• Baked chicken thighs with herb rub, roasted root vegetables
• Mixed green salad with grilled protein, olive oil and lemon dressing, seeds

Bone Broth Protocol

Chicken or beef bones (preferably organic, pasture-raised), 2 tablespoons apple cider vinegar (draws minerals from bones), filtered water to cover, onion, garlic, celery, peppercorns, bay leaf, salt. Simmer 12-24 hours (chicken) or 24-48 hours (beef) in slow cooker or stockpot. Strain, cool, refrigerate. Consume 1-2 cups daily warm, either as a drink or as a base for soups. Rich in glycine, proline, glutamine, collagen, and minerals.

Transition to Maintenance

The detox is a reset, not a lifestyle. The goal is to identify your optimal diet — the one that makes you feel best — and sustain it with reasonable flexibility.

The 80/20 Principle

Eat clean 80% of the time. Allow flexibility 20%. This is sustainable long-term. The 20% is not license to binge — it is room for social meals, travel, celebrations, and the imperfect reality of human life.

Ongoing Foundation

• Continue the core supplement stack (multivitamin, omega-3, magnesium, probiotics, vitamin D)
• Keep reactive foods out or rotate them (no more frequently than every 4 days)
• Maintain vegetable intake at 6+ cups daily
• Prioritize sleep (non-negotiable, always)
• Continue movement daily
• Repeat the full 21-day program seasonally (spring and fall) or when symptoms creep back
• Annual comprehensive lab work: CBC, CMP, lipids, thyroid, inflammatory markers, nutrient levels

The 21 days strip away the noise — the sugar, the processed food, the inflammation, the gut disruption — and reveal what your body actually feels like when it is not fighting its own inputs. Most people have never experienced that baseline. Once you have, you become your own most reliable diagnostic tool.

What would it mean to discover that “normal” is not how you are supposed to feel?