Unlock Ultimate Health: The Complete Guide to the Autoimmune Protocol (AIP) Diet

With food sensitivities and intolerances impacting a significant portion of the population, many individuals, especially those in the autoimmune disease and chronic illness communities, are exploring the role of diet in managing their conditions and improving their overall well-being. Elimination diets, when used thoughtfully and appropriately, can serve as powerful healing tools. The Autoimmune Protocol (AIP) diet is one such approach, designed to reduce inflammation and alleviate symptoms associated with autoimmune diseases.

Understanding Elimination Diets and the AIP

Elimination diets, also known as exclusion or healing diets, involve temporarily removing foods that may trigger adverse reactions in the body. The AIP diet is a specific type of elimination diet tailored for individuals with autoimmune conditions. It aims to identify and eliminate foods that may contribute to inflammation and immune system dysregulation, while simultaneously emphasizing the consumption of nutrient-dense foods to support healing and overall health.

The Core Principles of Elimination Diets

All elimination diets, including the AIP, follow a similar methodology:

Elimination: Temporarily exclude foods that are potentially problematic and may trigger symptoms. This phase typically lasts for a period of three to six weeks, or sometimes longer, depending on the specific protocol and individual needs.
Challenge: Systematically reintroduce the eliminated foods, one at a time, to observe the body's reaction to each food.
Reintroduction: Based on the body's responses during the challenge phase, determine which foods can be safely reintroduced into the diet and which should be avoided long-term.

Types of Elimination Diets

Several types of elimination diets exist, each with its own set of guidelines and target conditions. Some common examples include:

Low-FODMAP Diet: This diet restricts foods high in FODMAPs (fermentable oligo-, di-, and monosaccharides and polyols), which are a group of sugars that can be poorly digested and may contribute to gastrointestinal symptoms. It is often used to manage conditions like irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO).
Autoimmune Protocol (AIP) Diet: The AIP diet focuses on removing potentially inflammatory and immune-stimulating foods while emphasizing nutrient-dense foods to manage and treat autoimmune diseases. It also takes into account lifestyle factors in addition to diet.
Gut and Psychology/Physiology Syndrome (GAPS) Diet: This diet eliminates foods that are difficult to digest and incorporates nutritious whole foods to treat neurological and psychological conditions.
Specific Carbohydrate Diet (SCD): The SCD restricts grains and foods containing di- and polysaccharides while promoting the consumption of nutritious whole foods to balance the gut microbiome. It is often used to treat conditions like ulcerative colitis, Crohn's disease, and IBS.
Whole30: This diet removes potentially inflammatory and problematic foods such as grains, sugar, alcohol, and dairy.

The Autoimmune Protocol (AIP) Diet in Detail

The AIP diet is a stricter version of the Paleo diet and is designed to help treat all forms of autoimmune disease by eliminating certain food chemicals and compounds that cause gut dysbiosis and low-grade inflammation in sensitive individuals. It operates on the premise that autoimmune issues arise because of gut dysbiosis and low-grade inflammation of our cells.

The Three Phases of the AIP Diet

The AIP diet consists of three distinct phases:

Elimination Phase: This phase involves removing foods and medications believed to cause gut inflammation, imbalances between levels of good and bad bacteria in the gut, or an immune response.
Reintroduction Phase: Once a measurable improvement in symptoms and overall well-being occurs, the reintroduction phase can begin. During this phase, the avoided foods are gradually reintroduced into the diet, one at a time, based on the person’s tolerance.
Maintenance Phase: After you figure out which foods cause problems for you, you can create a long-term eating plan that avoids them.

Foods to Avoid During the Elimination Phase

During the elimination phase of the AIP diet, a wide range of foods are temporarily restricted, including:

Grains: Rice, wheat, oats, barley, rye, etc., as well as foods derived from them, such as pasta, bread, and breakfast cereals
Legumes: Lentils, beans, peas, peanuts, etc., as well as foods derived from them, such as tofu, tempeh, mock meats, or peanut butter
Nightshade vegetables: Eggplants, peppers, potatoes, tomatoes, tomatillos, etc., as well as spices derived from nightshade vegetables, such as paprika
Eggs: Whole eggs, egg whites, or foods containing these ingredients
Dairy: Cow’s, goat’s, or sheep’s milk, as well as foods derived from these milks, such as cream, cheese, butter, or ghee; dairy-based protein powders or other supplements should also be avoided
Nuts and seeds: All nuts and seeds and foods derived from them, such as flours, butter, or oils; also includes cocoa and seed-based spices, such as coriander, cumin, anise, fennel, fenugreek, mustard, and nutmeg
Certain beverages: Alcohol and coffee
Processed vegetable oils: Canola, rapeseed, corn, cottonseed, palm kernel, safflower, soybean, or sunflower oils
Refined or processed sugars: Cane or beet sugar, corn syrup, brown rice syrup, and barley malt syrup; also includes sweets, soda, candy, frozen desserts, and chocolate, which may contain these ingredients
Food additives and artificial sweeteners: Trans fats, food colorings, emulsifiers, and thickeners, as well as artificial sweeteners, such as stevia, mannitol, and xylitol

Some AIP protocols further recommend avoiding all fruit - both fresh or dried - during the elimination phase. Others allow the inclusion of 10-40 grams of fructose per day, which amounts to around 1-2 portions of fruit per day. Although not specified in all AIP protocols, some also suggest avoiding algae, such as spirulina or chlorella, during the elimination phase, as this type of sea vegetable may also stimulate an immune response.

Foods to Eat During the Elimination Phase

While the elimination phase may seem restrictive, there are still plenty of nutrient-dense foods to enjoy, including:

Vegetables: A variety of vegetables except for nightshade vegetables and algae, which should be avoided
Fresh fruit: A variety of fresh fruit, in moderation
Tubers: Sweet potatoes, taro, yams, as well as Jerusalem or Chinese artichokes
Minimally processed meat: Wild game, fish, seafood, organ meat, and poultry; meats should be wild, grass-fed or pasture-raised, whenever possible
Fermented, probiotic-rich foods: Nondairy-based fermented food, such as kombucha, sauerkraut, pickles, and coconut kefir; probiotic supplements may also be consumed
Minimally processed vegetable oils: Olive oil, avocado oil, or coconut oil
Herbs and spices: As long as they’re not derived from a seed or a chilli pepper
Vinegars: Balsamic, apple cider, and red wine vinegar, as long as they’re free of added sugars
Natural sweeteners: Maple syrup and honey, in moderation
Certain teas: Green and black tea at average intakes of up to 3-4 cups per day
Bone broth

Despite being allowed, some protocols further recommend that you moderate your intake of salt, saturated and omega-6 fats, natural sugars, such as honey or maple syrup, as well as coconut-based foods. Depending on the AIP protocol at hand, small amounts of fruit may also be allowed. This usually amounts to a maximum intake of 10-40 grams of fructose per day, or the equivalent of about 1-2 portions of fresh fruit. Some protocols further suggest moderating your intake of high glycemic fruits and vegetables, including dried fruit, sweet potatoes, and plantain. The glycemic index (GI) is a system used to rank foods on a scale of 0 to 100, based on how much they will increase blood sugar levels, compared with white bread. High glycemic fruits and vegetables are those ranked 70 or above on the GI scale (10).

The Reintroduction Phase: A Step-by-Step Guide

Once you have experienced a noticeable reduction in symptoms during the elimination phase, you can begin the reintroduction phase. This phase involves systematically reintroducing the eliminated foods, one at a time, to identify which foods trigger your symptoms and which are well-tolerated.

Here's a step-by-step approach to reintroducing foods:

Choose one food to reintroduce. Plan to consume this food a few times per day on the testing day, then avoid it completely for 5-6 days.
Eat a small amount, such as 1 teaspoon of the food, and wait 15 minutes to see if you have a reaction.
If you experience any symptoms, end the test and avoid this food. If you have no symptoms, eat a slightly larger portion, such as 1 1/2 tablespoons, of the same food and monitor how you feel for 2-3 hours.
If you experience any symptoms over this period, end the test and avoid this food. If no symptoms occur, eat a normal portion of the same food and avoid it for 5-6 days without reintroducing any other foods.
If you experience no symptoms for 5-6 days, you may reincorporate the tested food into your diet, and repeat this 5-step reintroduction process with a new food.

It’s best to avoid reintroducing foods under circumstances that tend to increase inflammation and make it difficult to interpret results. These include during an infection, following a poor night’s sleep, when feeling unusually stressed, or following a strenuous workout.

Additionally, it’s sometimes recommended to reintroduce foods in a particular order. For example, when reintroducing dairy, choose dairy products with the lowest lactose concentration to reintroduce first, such as ghee or fermented dairy products.

The Maintenance Phase: Creating a Sustainable Eating Plan

After you have completed the reintroduction phase and identified your individual food sensitivities, you can move on to the maintenance phase. This phase involves creating a long-term eating plan that avoids your trigger foods while incorporating a wide variety of nutrient-dense, well-tolerated foods.

Read also: The Hoxsey Diet

The maintenance phase emphasizes personalization, food diversity, and diet flexibility. The goal is to establish the broadest diet possible while maintaining tolerance and minimizing symptoms. You may find that you can occasionally indulge in a trigger food for special events, as long as the consequences aren't too serious. It's also possible for your body's response to change over time, so you can always go back to the reintroduction phase with a particular food, although it's best to wait at least a year.

Potential Benefits of the AIP Diet

While research on the AIP diet is still limited, some evidence suggests that it may offer several potential benefits for individuals with autoimmune diseases.

May Help Heal a Leaky Gut

People with autoimmune diseases often have a leaky gut, and experts believe there may be a link between the inflammation they experience and the permeability of their gut. By removing potentially inflammatory foods and emphasizing nutrient-dense foods, the AIP diet may help to heal the gut lining and reduce intestinal permeability.

May Reduce Inflammation and Symptoms of Some Autoimmune Disorders

To date, the AIP diet has been tested in a small group of people and yielded seemingly positive results. For instance, in a recent 11-week study in 15 people with IBD on an AIP diet, participants reported experiencing significantly fewer IBD-related symptoms by the end of the study. However, no significant changes in markers of inflammation were observed (15). Similarly, a small study had people with IBD follow the AIP diet for 11 weeks. Participants reported significant improvements in bowel frequency, stress, and the ability to perform leisure or sport activities as early as 3 weeks into the study (6). In another study, 16 women with Hashimoto’s thyroiditis, an autoimmune disorder affecting the thyroid gland, followed the AIP diet for 10 weeks. By the end of the study, inflammation and disease-related symptoms decreased by 29% and 68%, respectively. Participants also reported significant improvements in their quality of life, despite there being no significant differences in their measures of thyroid function (7).

Managing Autoimmune Disorders

Rheumatoid Arthritis: Rheumatoid arthritis (RA) is a systemic autoimmune condition involving inflammation in joints that causes pain, swelling, stiffness, and sometimes joint deformities. Only one small controlled study in 2023 studied the benefits of the AIP diet in people with rheumatoid arthritis. Although the results were promising for reducing symptoms of RA using the AIP diet, additional research is needed.
Inflammatory Bowel Disease: A few studies have observed benefits with the Autoimmune Protocol for people with inflammatory bowel disease (IBD). In one study of individuals with ulcerative colitis (UC), a type of IBD, the AIP diet reduced inflammatory markers. Another study found that participants with either UC or Crohn’s disease experienced improved quality of life after following the AIP diet. However, further investigation is needed.
Improving Overall Health Gut Health and Leaky Gut: Research suggests that autoimmunity has its origins in a response to stress, be it psychological or physiological. Stress disrupts the function of the intestinal barrier, a process called “leaky gut,” leading to an autoimmune response in the body. Although autoimmune processes are often accompanied by a leaky gut, experts do not yet have consensus on whether or not there is a definite cause-and-effect relationship between these two processes.
Long-term Quality of Life: For those struggling with an autoimmune condition, symptoms can be debilitating. It is important to find ways to manage the condition by reducing symptoms. While the AIP diet can be challenging to follow due to its restrictive nature in the elimination phase, it may be worth it in the long term. Research shows that the AIP diet helps improve quality of life for individuals with Hashimoto’s thyroiditis and IBD. However, no changes in disease markers, like thyroid function or thyroid antibodies, were shown. Additionally, the goal of AIP is to not be so restrictive forever but instead to reintroduce food, with the goal of establishing the broadest diet possible while maintaining tolerance. For those struggling with autoimmunity, there is potential for flares to occur, especially during stressful times. Returning to the elimination phase of the AIP diet during those times may be useful.

Potential Risks and Considerations

While the AIP diet may offer potential benefits, it is important to be aware of the potential risks and considerations associated with this restrictive eating plan.

Nutrient Deficiencies: The elimination phase of the AIP diet can be very restrictive, which may increase the risk of nutrient deficiencies if not carefully planned.
Social Isolation: The restrictive nature of the AIP diet can make it difficult to eat in social situations, such as at restaurants or friend's houses, potentially leading to social isolation.
Not a Guaranteed Solution: There's no guarantee that the AIP diet will reduce inflammation or disease-related symptoms in all people with autoimmune disorders.
Potential for Disordered Eating: Elimination diets, including the AIP, may not be the best approach for everyone-particularly for those with a history of eating disorders or disordered eating.
Difficulty Meeting Nutrient Requirements: Remaining in the elimination phase for too long can make it difficult to meet your daily nutrient requirements, potentially increasing your risk of developing nutrient deficiencies and poor health over time.
The AIP diet is considered an elimination diet, which makes it very restrictive and potentially hard to follow for some, especially in its elimination phase.
The elimination phase of this diet can also make it difficult for people to eat in social situations, such as at a restaurant or friend’s house, increasing the risk of social isolation.
It’s also important to note that there’s no guarantee that this diet will reduce inflammation or disease-related symptoms in all people with autoimmune disorders. However, those who experience a reduction in symptoms following this diet may be reticent to progress to the reintroduction phase, for fear it may bring the symptoms back. This could become problematic, as remaining in the elimination phase can make it difficult to meet your daily nutrient requirements. Therefore, remaining in this phase for too long may increase your risk of developing nutrient deficiencies, as well as poor health over time. This is why the reintroduction phase is crucial and should not be skipped. If you’re experiencing difficulties getting started with the reintroduction phase, consider reaching out to a registered dietitian or other medical professional knowledgeable about the AIP diet for personalized guidance.

Who Should Avoid the AIP Diet?

The AIP diet may not be suitable for everyone. Certain individuals should avoid this restrictive eating plan, including:

Pregnant women
People who are underweight
People who are malnourished
Individuals with a history of eating disorders

In these situations, it's best to consult with a healthcare professional to determine a safer and more appropriate dietary approach.

Tips for Success on the AIP Diet

If you decide to try the AIP diet, there are several strategies you can implement to increase your chances of success.

Plan Ahead

The AIP diet requires significant dietary changes, so it's important to have a plan in place before you begin. This includes:

Creating a Weekly Meal Plan: The limited food options when following the AIP diet can make choosing what to eat for meals challenging. To make it easier, create a weekly meal plan ahead of time. Build your meal by starting with a protein source like meat, poultry, or fish. Choose a variety of veggies and add an AIP-approved carbohydrate source, such as sweet potato, plantains, or fruit. Add healthy fats like avocado or olive oil for flavor and added nutrition.
Batch Cooking: To make it even easier to follow the AIP diet plan, consider batch cooking. Batch cooking means preparing large portions of foods to be used as leftovers. Plan to batch cook a few protein sources each week, such as oven-baked or grilled chicken and fish and ground beef cooked in a skillet. Next, chop a variety of veggies - roast or steam half of them and leave the other half raw for salads or snacks. Also batch cook starches such as sweet potatoes and plantains. Use your batch-cooked foods to easily put together a variety of dishes throughout the week to keep things exciting.
AIP Recipe Ideas: An example of an AIP-approved breakfast could be sausage and sweet potato hash made with a mix of cooked ground meat with roasted sweet potato pieces and a side of avocado. For lunch, prepare a salad of chopped cooked chicken and add to a bed of leafy greens and veggies. Top with a drizzle of olive oil and apple cider vinegar for dressing, and serve with fruit on the side. For dinner, pair cooked fish with roasted veggies and homemade sweet potato fries. Finish with a dessert of coconut yogurt sweetened with berries.

Seek Professional Guidance

Working with a registered dietitian or other qualified healthcare professional can provide valuable support and guidance throughout your AIP journey. A dietitian can help you:

Create an AIP-approved meal plan that meets your individual nutritional needs
Navigate the elimination and reintroduction phases
Identify your trigger foods
Develop a sustainable long-term eating plan
Address any challenges or concerns you may have

Track Your Progress

Keeping a food diary to regularly track any changes in symptoms as you follow the elimination phase as well as when reintroducing foods. Document any improvements or flare-ups, including details like pain levels, digestive issues, skin changes, and energy levels. Plan regular check-ins with your healthcare provider or dietitian to help you assess progress and make any necessary adjustments.

Find Support

Since following the AIP diet requires quite a bit of change in your day to day routine, joining a support group can help. There are AIP support groups online that discuss meal planning tips, share recipes, and offer support for navigating challenging situations.

Navigate Social Situations

Before dining out, take a look at online restaurant menus for AIP-friendly options. You can also call ahead to ask if the restaurant can accommodate special dietary requests. Look for dishes prepared with simple cooking methods such as grilling and steaming. Opt for simple dishes like grilled meats, steamed or roasted vegetables, and salads.

Talk to your restaurant server and explain your dietary needs, emphasizing that you need to avoid specific ingredients. If it’s not clear on the menu, ask the server to verify with the chef which ingredients are used in dishes that you are considering.

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