What Is the AIP Diet? Autoimmune Protocol Explained
The Autoimmune Protocol (AIP) is an elimination diet designed to reduce inflammation, calm overactive immune responses, and help people with autoimmune conditions identify the foods that trigger their symptoms. Built as a stricter extension of the standard Paleo diet, AIP removes foods that are most likely to irritate the gut lining and provoke immune reactions, then reintroduces them one at a time so you can pinpoint your personal triggers.
If you live with an autoimmune condition such as Hashimoto's thyroiditis, rheumatoid arthritis, inflammatory bowel disease (IBD), psoriasis, or lupus, the AIP diet offers a structured, evidence-based framework for using food as a tool in your overall management plan. This guide covers exactly what the protocol involves, what the research says, and how to follow it safely.
For a broader look at how dietary patterns influence autoimmune conditions, see our guide on anti-inflammatory diets for autoimmune conditions.
The Science Behind AIP
Autoimmune diseases share a common mechanism: the immune system mistakenly attacks the body's own tissues. While genetics load the gun, environmental factors pull the trigger. Among those environmental factors, diet plays a significant role through several pathways.
Intestinal Permeability (Leaky Gut)
Research published in Physiological Reviews has established that increased intestinal permeability is a precondition for autoimmune disease development (Fasano, 2012). When the tight junctions between cells in the intestinal lining become compromised, partially digested food proteins, bacterial toxins, and other molecules pass into the bloodstream. The immune system recognizes these molecules as foreign invaders and mounts an inflammatory response.
Certain food compounds are known to increase intestinal permeability. Gluten, for example, triggers the release of zonulin, a protein that directly opens tight junctions in the gut lining. Alcohol and processed food additives like emulsifiers (polysorbate 80, carboxymethylcellulose) have similar effects, as demonstrated in research from Georgia State University (Chassaing et al., 2015).
Lectins, Saponins, and Other Plant Defense Chemicals
Plants produce compounds like lectins, saponins, and glycoalkaloids to defend against predators. In concentrated amounts, these compounds can damage the intestinal lining and stimulate the immune system. Nightshade vegetables (tomatoes, peppers, potatoes, eggplant) contain glycoalkaloids such as solanine and tomatine. Legumes contain high concentrations of lectins, particularly phytohaemagglutinin. Grains contain both lectins (wheat germ agglutinin) and other potentially irritating proteins.
AIP removes these foods during the elimination phase to give the gut lining time to heal and the immune system a chance to calm down.
Molecular Mimicry
Some food proteins share structural similarities with human tissues. When these proteins cross a compromised gut barrier, the antibodies produced against them may also attack the body's own cells. This process, called molecular mimicry, has been documented between dairy proteins (specifically butyrophilin) and myelin in multiple sclerosis, and between gluten peptides and thyroid tissue in Hashimoto's thyroiditis (Vojdani, 2015).
To understand more about the connection between chronic inflammation and disease progression, read our ultimate guide to inflammation and disease.
Phase 1: The Elimination Phase
The elimination phase is the core of the AIP protocol. During this period, lasting 30 to 90 days (or until symptoms noticeably improve), you remove all potentially inflammatory foods while focusing on nutrient-dense, healing options.
Foods to Eliminate
- Grains: All grains including wheat, rice, oats, corn, barley, and pseudo-grains like quinoa and buckwheat
- Legumes: Beans, lentils, chickpeas, peanuts, soy, and all soy-derived products
- Dairy: All forms including milk, cheese, yogurt, butter, ghee, and whey protein
- Eggs: Both whites and yolks (egg whites are the primary concern due to lysozyme and other proteins that can cross the gut barrier)
- Nuts and seeds: All tree nuts, seeds, and seed-derived spices (cumin, coriander, fennel, mustard, nutmeg)
- Nightshade vegetables: Tomatoes, peppers (bell and hot), eggplant, white potatoes, goji berries, and nightshade-derived spices (paprika, cayenne, chili powder)
- Refined sugars and artificial sweeteners: Including high-fructose corn syrup, aspartame, sucralose, and sugar alcohols
- Alcohol and coffee: Both are gut irritants; coffee stimulates the adrenal stress response even in decaf form
- Food additives: Emulsifiers, thickeners, artificial colors, and preservatives
- NSAIDs: While not a food, non-steroidal anti-inflammatory drugs like ibuprofen damage the gut lining and are discouraged during AIP
For a step-by-step approach to running elimination diets effectively, see our article on elimination diets and finding your inflammatory triggers.
Foods to Eat
AIP is not just about restriction. The protocol places heavy emphasis on nutrient density.
- Quality meats: Grass-fed beef, lamb, bison, wild game, and pasture-raised poultry
- Organ meats: Liver, heart, and kidney (among the most nutrient-dense foods available)
- Wild-caught seafood: Salmon, sardines, mackerel, shellfish, and other fatty fish rich in omega-3 fatty acids
- Vegetables: All non-nightshade vegetables, with emphasis on leafy greens, cruciferous vegetables (broccoli, cauliflower, Brussels sprouts), root vegetables (sweet potatoes, beets, carrots, parsnips), and alliums (onions, garlic, leeks)
- Fruits: All whole fruits in moderation, especially berries for their polyphenol content
- Healthy fats: Olive oil, coconut oil, avocado oil, and animal fats from quality sources
- Fermented foods: Sauerkraut, kimchi (nightshade-free), coconut yogurt, and kombucha for probiotic support
- Bone broth: Rich in collagen, glycine, and minerals that support gut lining repair
- Fresh herbs and AIP-compliant spices: Basil, oregano, thyme, rosemary, turmeric, ginger, cinnamon (from Ceylon, not cassia). Our anti-inflammatory spice guide covers which spices deliver the most benefit and how to use them.
For a broader list of foods that fight inflammation, check out our complete list of anti-inflammatory foods.
Phase 2: Systematic Reintroduction
The reintroduction phase is where the real personalization happens. After the elimination period, you bring foods back one at a time, in a specific order, monitoring your body's response at each step. Skipping this phase means you stay on an unnecessarily restrictive diet without learning which foods actually affect you.
Reintroduction Order
Foods are typically reintroduced from least likely to provoke a reaction to most likely:
Stage 1 (least likely to cause issues): Egg yolks, ghee, seed-based spices (cumin, coriander), fruit-based spices (black pepper), legumes with edible pods (green beans, sugar snap peas)
Stage 2: Seeds (flax, chia, sunflower, pumpkin), nuts (macadamia first, then others), cocoa and chocolate, alcohol in small amounts
Stage 3: Eggs (whole), nightshades (starting with peeled and cooked potatoes, then cooked tomatoes, then peppers), coffee, grass-fed butter and cream
Stage 4 (most likely to cause issues): Gluten-free grains (white rice first), legumes (lentils first), dairy (fermented forms like yogurt and kefir first), white potatoes with skin, alcohol in larger amounts
The Reintroduction Protocol
For each food, follow this process:
- Day 1: Eat a small amount of the food (about half a teaspoon). Wait 15 minutes. If no immediate reaction, eat a slightly larger portion. Wait another 15 minutes, then eat a normal serving size.
- Days 2 through 4: Do not eat the food again. Monitor for symptoms including digestive upset, joint pain, skin changes, fatigue, headaches, mood shifts, and sleep disturbances.
- Day 5: If no symptoms appeared, the food can be considered safe for now. Add it back to your regular rotation and move on to the next food.
Keep a detailed food and symptom journal throughout this process. Changes can be subtle, so writing everything down helps you catch patterns you might otherwise miss.
Clinical Evidence for AIP
The AIP diet has moved beyond anecdotal support. Several clinical studies now provide evidence for its effectiveness.
Inflammatory Bowel Disease
The most cited AIP study was conducted by Konijeti et al. and published in Inflammatory Bowel Diseases in 2017. This clinical trial enrolled 15 patients with active Crohn's disease and ulcerative colitis. After six weeks on the AIP elimination diet, 11 of the 15 participants (73%) achieved clinical remission. Endoscopic improvements were also documented in several patients. These results were maintained through the maintenance phase of the study.
Hashimoto's Thyroiditis
A 2019 study published in Cureus examined 16 women with Hashimoto's thyroiditis who followed the AIP diet for 10 weeks. Researchers found significant improvements in quality of life scores and a reduction in systemic inflammation, measured by high-sensitivity C-reactive protein (hs-CRP). While thyroid antibody levels did not change significantly in this short timeframe, symptom burden decreased substantially (Abbott et al., 2019).
Broader Autoimmune Research
Pilot studies and case series have explored AIP's effects on conditions including psoriasis, rheumatoid arthritis, and multiple sclerosis. A pilot study presented at the American College of Rheumatology annual meeting showed measurable reductions in disease activity scores in RA patients following AIP for 90 days. While larger randomized controlled trials are still needed, the existing evidence consistently points toward meaningful symptom reduction.
For more on how gut health connects to systemic inflammation and autoimmunity, read our article on anti-inflammatory foods for gut health.
A Sample 3-Day AIP Meal Plan
Day 1
- Breakfast: Sweet potato hash with ground turkey, sauteed kale, and diced onions cooked in coconut oil. Fresh berries on the side.
- Lunch: Large salad with mixed greens, shredded carrots, sliced beets, avocado, grilled salmon, and olive oil with lemon dressing.
- Dinner: Slow-cooked beef stew with carrots, parsnips, celery, and fresh thyme. Side of roasted broccoli with garlic.
- Snack: Coconut yogurt with a handful of blueberries.
Day 2
- Breakfast: Chicken and vegetable soup made with bone broth, spinach, zucchini, and fresh ginger. One banana.
- Lunch: Lettuce wraps filled with ground pork, shredded cabbage, grated ginger, green onions, and coconut aminos.
- Dinner: Baked wild-caught cod with roasted asparagus and mashed cauliflower with olive oil and fresh chives.
- Snack: Sliced apple with a thin spread of tigernut butter (tigernuts are tubers, not true nuts).
Day 3
- Breakfast: Pan-fried sardines over arugula with sliced avocado, fresh dill, and a squeeze of lemon. Roasted plantain slices.
- Lunch: Turkey burger (no bun) with caramelized onions, sauteed mushrooms, and a large side of roasted Brussels sprouts.
- Dinner: Lamb chops with mint sauce (fresh mint, olive oil, garlic, and apple cider vinegar). Roasted root vegetable medley with sweet potatoes, turnips, and beets.
- Snack: Homemade bone broth with a pinch of sea salt and fresh turmeric.
Common Mistakes on AIP
Treating it as a permanent diet. AIP is a diagnostic tool, not a lifelong eating plan. The elimination phase is temporary. The goal is always to reintroduce as many foods as your body tolerates. Staying on the full elimination protocol indefinitely can lead to unnecessary dietary restriction and potential nutrient gaps.
Rushing reintroductions. Introducing multiple foods at once, or not waiting long enough between reintroductions, makes it impossible to identify which food caused a reaction. Patience during this phase is critical.
Ignoring non-food factors. Diet is one piece of the autoimmune puzzle. Sleep deprivation, chronic stress, lack of physical activity, and environmental toxins all influence immune function and inflammation. AIP works best as part of a comprehensive lifestyle approach. For the bigger picture on how food and inflammation interact, our beginner's guide to the anti-inflammatory diet is a good starting point.
Not eating enough. Because so many food groups are restricted, some people unintentionally under-eat. This creates a caloric deficit that raises cortisol, increases inflammation, and undermines the entire purpose of the protocol. Plan meals carefully and eat generous portions of allowed foods.
Skipping organ meats and seafood. These foods provide concentrated doses of zinc, selenium, vitamin A, omega-3 fatty acids, and other nutrients essential for immune regulation and gut repair. Without them, the nutrient density advantage of AIP is significantly reduced. If you are curious about why omega-3s matter so much, see our breakdown of omega-6 vs. omega-3 and the inflammation ratio.
Who Should (and Shouldn't) Try AIP
AIP is most appropriate for people with diagnosed autoimmune conditions who have not responded adequately to conventional treatment alone, or who want to explore dietary factors alongside medical care. It can be particularly helpful for:
- Inflammatory bowel disease (Crohn's and ulcerative colitis)
- Hashimoto's thyroiditis and Graves' disease
- Rheumatoid arthritis
- Psoriasis and eczema
- Celiac disease (AIP goes beyond gluten-free)
- Multiple sclerosis
- Lupus (systemic lupus erythematosus)
AIP may not be appropriate for people with a history of eating disorders, as the restrictive elimination phase can trigger disordered eating patterns. Children, pregnant women, and people who are underweight should only attempt AIP under close supervision from a healthcare provider and a registered dietitian experienced with elimination protocols.
AIP is not a replacement for medical treatment. It is a complementary strategy that works alongside your doctor's care. Always discuss major dietary changes with your healthcare team, especially if you take medications that interact with dietary changes (such as warfarin, which is affected by vitamin K intake).
AIP Diet Food List: What You Can and Cannot Eat
Having a clear, comprehensive food list makes the elimination phase dramatically easier. We put this together as a quick-reference guide you can pull up on your phone at the grocery store or tape to your refrigerator.
Proteins (all allowed):
- Grass-fed beef, bison, lamb, venison, and elk
- Pasture-raised chicken, turkey, and duck
- Wild-caught salmon, sardines, mackerel, cod, halibut, shrimp, scallops, mussels, and oysters
- Organ meats: liver, heart, kidney (aim for 2 to 3 servings per week)
- Bone broth from any of the above
Vegetables (allowed, non-nightshade):
- Leafy greens: spinach, kale, arugula, collards, Swiss chard, romaine, watercress
- Cruciferous: broccoli, cauliflower, Brussels sprouts, cabbage, bok choy
- Root vegetables: sweet potatoes, beets, carrots, parsnips, turnips, rutabaga
- Alliums: onions, garlic, leeks, shallots, chives
- Others: zucchini, cucumber, celery, asparagus, artichokes, mushrooms, squash (all types)
Fruits (all allowed in moderation):
- Berries: blueberries, strawberries, raspberries, blackberries
- Citrus: oranges, lemons, limes, grapefruit
- Others: apples, bananas, plantains, mangoes, pears, figs, dates, coconut (all forms)
Fats and oils (allowed):
- Extra virgin olive oil, coconut oil, avocado oil, palm oil (sustainably sourced)
- Animal fats: lard, tallow, duck fat from quality sources
- Whole avocados and olives
Fermented foods (allowed):
- Sauerkraut (no nightshade seasonings), kimchi (nightshade-free), coconut yogurt, kombucha, water kefir, apple cider vinegar
Herbs and spices (allowed):
- Fresh and dried: basil, oregano, thyme, rosemary, sage, mint, dill, parsley, cilantro, lemongrass
- Turmeric, ginger, cinnamon (Ceylon), garlic powder, onion powder
- Sea salt, apple cider vinegar, coconut aminos
Foods to eliminate completely:
- All grains (wheat, rice, oats, corn, quinoa, buckwheat)
- All legumes (beans, lentils, chickpeas, peanuts, soy)
- All dairy (milk, cheese, yogurt, butter, ghee, whey)
- Eggs (whites and yolks)
- All nuts and seeds (including seed-based spices like cumin, coriander, mustard, nutmeg)
- Nightshades (tomatoes, peppers, eggplant, white potatoes, goji berries, paprika, cayenne)
- Refined sugars, artificial sweeteners, and sugar alcohols
- Alcohol, coffee (including decaf)
- Food additives, emulsifiers, and artificial colors
AIP Diet Recipes: Simple Meals for Every Day
One of the biggest hurdles on AIP is figuring out what to actually cook. These six recipes use only AIP-compliant ingredients and take 30 minutes or less. None of them feel like "restriction food."
1. Lemon-Herb Salmon with Roasted Sweet Potatoes Season a salmon fillet with olive oil, lemon juice, fresh dill, and sea salt. Bake at 400F for 12 to 15 minutes. Meanwhile, cube sweet potatoes, toss with olive oil and rosemary, and roast on a sheet pan alongside the fish. Serve over a bed of arugula. This is a 20-minute meal with omega-3s, beta-carotene, and polyphenols in one plate.
2. Turkey and Vegetable Stir-Fry with Coconut Aminos Brown ground turkey in coconut oil with minced garlic and fresh ginger. Add shredded cabbage, sliced zucchini, shredded carrots, and sliced mushrooms. Splash with coconut aminos and cook until vegetables are tender-crisp. Serve over cauliflower rice. The whole thing comes together in 15 minutes.
3. Bone Broth Soup with Root Vegetables Bring 4 cups of bone broth to a simmer. Add diced carrots, parsnips, celery, and sweet potato. Season with turmeric, thyme, and sea salt. Simmer 20 minutes until vegetables are soft. Stir in a generous handful of chopped kale in the last 3 minutes. This is the ideal flare-day meal: gentle on digestion, packed with minerals, and soothing.
4. Herb-Crusted Chicken Thighs with Brussels Sprouts Mix minced garlic, chopped rosemary, fresh thyme, olive oil, and sea salt into a paste. Rub over bone-in chicken thighs. Arrange on a sheet pan with halved Brussels sprouts. Roast at 425F for 25 to 30 minutes. The chicken skin gets crispy and the Brussels sprouts caramelize. One pan, minimal cleanup.
5. Sardine and Avocado Salad Drain a can of sardines and place over a large bed of mixed greens (arugula, spinach, romaine). Add sliced avocado, thinly sliced red onion, shaved beets, and fresh dill. Dress with olive oil and lemon juice. This no-cook meal takes 5 minutes and delivers one of the highest nutrient densities per calorie of any AIP meal.
6. Coconut-Ginger Chicken Soup Simmer chicken breast in coconut milk with fresh ginger, garlic, lemongrass, and turmeric. After 15 minutes, shred the chicken directly in the pot. Add sliced mushrooms and baby spinach. Season with sea salt and a squeeze of lime. Serve in deep bowls. Rich, warming, and anti-inflammatory.
For more recipe inspiration that works within elimination frameworks, see our anti-inflammatory smoothie recipes (most are easily adapted to AIP by swapping out any non-compliant ingredients).
AIP Diet Meal Plan: A Sample Week
The 3-day plan above gives you a starting point, but a full week of planned meals removes guesswork and helps you build momentum. Here is a complete 7-day framework. Batch-cooking on Sunday makes the rest of the week much simpler.
Sunday Prep Session (60 to 90 minutes): Roast a large batch of sweet potatoes and root vegetables. Cook 2 pounds of ground turkey or chicken thighs. Make a pot of bone broth if you do not have any stored. Wash and prep salad greens for the week.
Monday:
- Breakfast: Sweet potato hash with ground turkey, sauteed kale, and diced onions in coconut oil. Fresh berries.
- Lunch: Large salad with mixed greens, shredded carrots, beets, avocado, and canned salmon. Olive oil and lemon dressing.
- Dinner: Lemon-herb salmon with roasted Brussels sprouts and mashed cauliflower.
Tuesday:
- Breakfast: Chicken and vegetable bone broth soup (from prep) with a banana.
- Lunch: Lettuce wraps with ground pork, shredded cabbage, ginger, green onions, and coconut aminos.
- Dinner: Herb-crusted chicken thighs with roasted root vegetable medley (carrots, parsnips, turnips).
Wednesday:
- Breakfast: Coconut yogurt with blueberries and a drizzle of raw honey. Side of leftover sweet potato.
- Lunch: Sardine and avocado salad over arugula with olive oil dressing.
- Dinner: Turkey and vegetable stir-fry with cauliflower rice.
Thursday:
- Breakfast: Pan-fried plantains with ground breakfast sausage (AIP-compliant, no nightshade spices) and sauteed spinach.
- Lunch: Leftover turkey stir-fry, reheated, with extra greens.
- Dinner: Baked cod with roasted asparagus, mashed sweet potato, and fresh chives.
Friday:
- Breakfast: Smoothie made with coconut milk, frozen mixed berries, a handful of spinach, collagen peptides, and fresh ginger.
- Lunch: Bone broth soup with leftover vegetables and shredded chicken.
- Dinner: Lamb chops with mint sauce (fresh mint, olive oil, garlic, apple cider vinegar), roasted beets, and sauteed Swiss chard.
Saturday:
- Breakfast: Sweet potato "toast" (thick slices, toasted) topped with avocado and smoked salmon.
- Lunch: Large mixed greens salad with grilled chicken, shaved carrots, cucumber, and olive oil-lemon dressing.
- Dinner: Coconut-ginger chicken soup with mushrooms and baby spinach. Side of roasted plantain chips.
Sunday:
- Breakfast: Leftover soup or bone broth with fresh fruit.
- Lunch: Use up remaining proteins and vegetables from the week in a big bowl with olive oil.
- Dinner: Start the cycle fresh, or try a new recipe.
- Afternoon: Batch-cook and prep for the coming week.
Snack options throughout the week: Coconut yogurt with berries, sliced apple, plantain chips with guacamole, bone broth, fresh fruit, or leftover protein and vegetables. Keep portions of these ready in the fridge so you are not scrambling when hunger hits.
For more structured meal planning guidance, our 7-day anti-inflammatory meal plan offers a full week of recipes (many of which can be adapted for AIP compliance).
Frequently Asked Questions
What can you eat on the AIP diet?
AIP allows all quality meats (grass-fed beef, poultry, wild game), wild-caught seafood, non-nightshade vegetables, fruits, healthy fats (olive oil, coconut oil, avocado oil), fermented foods like sauerkraut and coconut yogurt, bone broth, and fresh herbs. The emphasis is on nutrient density: organ meats, fatty fish, and colorful vegetables form the foundation. See the comprehensive food list above for the full breakdown.
Is the AIP diet the same as Paleo?
AIP is a stricter version of Paleo. Standard Paleo allows eggs, nuts, seeds, nightshades, and coffee. AIP removes all of these during the elimination phase because they contain compounds that may irritate the gut lining or stimulate immune responses in people with autoimmune conditions. After the elimination phase, many of these foods get reintroduced. Think of AIP as Paleo with an extra layer of caution for people whose immune systems need more support.
How much does the AIP diet cost?
AIP can be more expensive than a standard diet because it emphasizes quality meats and fresh produce while eliminating cheap staples like grains and legumes. However, you can manage costs. Buy frozen vegetables and berries (same nutrition, lower price). Use canned wild salmon and sardines instead of fresh fish. Buy whole chickens and use the bones for broth. Batch-cooking and meal prepping also reduce waste and impulse spending. Budget roughly 15 to 25% more than your current grocery spending.
Can you do AIP as a vegetarian?
This is very difficult. AIP eliminates legumes, grains, eggs, dairy, nuts, and seeds, which are the primary protein sources for most vegetarians. The protocol relies heavily on animal protein and organ meats for nutrient density. Some practitioners have developed modified vegetarian-leaning AIP approaches, but these require careful planning with a registered dietitian to avoid serious nutrient deficiencies. If you have strong ethical reasons for avoiding meat, discuss alternatives with a practitioner experienced in both AIP and plant-based nutrition.
When should I start reintroducing foods?
Start reintroductions after a minimum of 30 days on strict elimination, and only after you have noticed meaningful symptom improvement. Some people need 60 to 90 days. If you have not seen any improvement after 90 days, the foods you eliminated may not be your primary triggers, and it is worth investigating other factors (stress, sleep, environmental exposures) with your healthcare team.
The Bottom Line
The Autoimmune Protocol is a structured, science-informed approach to identifying food-based triggers of autoimmune inflammation. By temporarily removing the most common immune-provoking foods and then carefully reintroducing them, AIP helps you build a personalized, sustainable diet that supports your immune health over the long term. The clinical evidence, while still growing, consistently demonstrates meaningful improvements in symptoms and quality of life for people with autoimmune conditions.
The key to success with AIP is treating it as a process of discovery rather than a set of permanent rules. Work with a knowledgeable practitioner, track your responses diligently, and reintroduce foods systematically. The result is a way of eating tailored to your body's specific needs.
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Vojdani, A. (2015). "Molecular mimicry as a mechanism for food immune reactivities and autoimmunity." Alternative Therapies in Health and Medicine, 21 Suppl 1, 34-45. https://pubmed.ncbi.nlm.nih.gov/25599185/
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Konijeti, G.G., et al. (2017). "Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease." Inflammatory Bowel Diseases, 23(11), 2054-2060. https://pubmed.ncbi.nlm.nih.gov/28858071/
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Abbott, R.D., et al. (2019). "Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis." Cureus, 11(4), e4556. https://pubmed.ncbi.nlm.nih.gov/31275780/
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