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The Ultimate Guide To Autoimmune Protocol aka The AIP Diet

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If you suffer from an autoimmune disease, then you know that managing your symptoms and getting to where you’re feeling ‘normal’ and like yourself feels like a never-ending struggle. An AIP Diet might be right for you.

Between the medications and possibly even surgeries, it may seem that you’re stuck with very invasive options that don’t necessarily have a big impact on improving your disease.

The Autoimmune Protocol (AIP) was designed to help reduce the inflammation in your body to relieve the symptoms of autoimmune disorders.

It is a relatively new, food-based approach with the aim to heal your gut and in doing so, reduce inflammation.

Autoimmune conditions begin in the gut. In order to heal your body, you need to heal your gut first.

While I’m not saying that the Autoimmune Protocol is going to be your next ‘miracle cure’, I will say that if you want to really focus on your healing, this is an excellent way to start.

Before we get deeper into the topic, I want to be clear. The AIP diet is not a weight loss diet. Nor is it a fad diet.

It is a therapeutic diet. This means that it’s not just something you pick up and do for fun for a few weeks, like trying to cut out bread or drink “detox juices”. This a full-on lifestyle change.

Learn how to adopt a keto diet if starting AIP feels too much at first.

What Is The AIP Diet?

Autoimmune Diseases

An autoimmune disease is one where your immune system attacks healthy cells. The job of your immune system is to guard against germs like bacteria and viruses. When the immune system detects these germs, it sends out fighter cells to attack them.

The problem comes in when your immune system mistakenly sends out these fighter cells to attack good, healthy cells.

Rheumatoid arthritis, lupus, celiac disease, and multiple sclerosis are common autoimmune diseases. The immune system attacks healthy cells in different ways, depending on the disease.

Rheumatoid arthritis is a chronic inflammatory disorder that affects many joints, including those in the hands and feet.

For those suffering from lupus, what is happening is that the immune system is attacking its own tissues. And with multiple sclerosis, the immune system is actually eating away at the protective covering of the nerves.

There are over 80 known illnesses caused by autoimmunity, and in the US alone over 50 million people suffer from an autoimmune disease.

It is quite a scary thought – our own bodies turning against us. And what makes it worse is that we still don’t have a good idea of why it happens, and how to prevent or cure it.

For those suffering from an autoimmune disorder, it can also be a confusing, stressful, and even depressing time – in addition to being painful and uncomfortable. With often no hope of any recovery.

While the science and medical communities are still working on figuring out why this happens, and trying to develop cures for it, there are steps you can take now to reduce or slow down the symptoms.

Treatments for autoimmune disorders are focused on controlling the overactive immune response, healing the gut, and reducing inflammation.

In addition to treatments, there is another way you can help reduce inflammation in your body – through your diet.

Healing Through Elimination

The Autoimmune Protocol (AIP) diet is designed specifically to reduce inflammation in your body, thereby helping to relieve your body of the symptoms of your autoimmune disease. It also helps to heal gut dysfunction.

The AIP diet is based on the belief that autoimmune disorders are caused by small holes in the gut that cause toxins and bacteria to leak into the body (commonly known as “leaky gut”, and medically known as “intestinal permeability”).

The AIP diet is an elimination focused on including nutrient-dense foods while eliminating foods that cause (or can potentially cause) an inflammatory or allergic reaction.

The theory is that by eliminating certain foods and food chemicals, it gives the body the chance to recover and “reset” (known medically as remission), and allows the gut to heal.

When a celiac disease patient cuts out gluten – that is elimination. Or when an IBS sufferer follows the low FODMAP diet. It is the same concept.

What is an elimination diet?

An elimination diet involves removing certain foods from your diet (often for a set period of time, like 4 weeks). An elimination diet can be done for two reasons – to help your body have a chance to heal or to pinpoint specific foods that cause inflammation, allergies, or other symptoms.

After the set period of elimination, some foods are allowed back into the diet. This is called “reintroduction”. While you are reintroducing these foods, it is important to closely monitor your reactions to them.

The foods that are eliminated aren’t “bad” – they are just possible irritants. And the only way to find out if they are irritants is to eliminate them for a while. Anything you eat has the ability to heal or harm you – it is important to not see foods as “good” or “bad”. Our bodies just react to them in different ways.

Your body will let you know what it can tolerate – and how much. You will know which foods your body cannot tolerate, and stay away from them.

Because this diet doesn’t target a specific disease, but rather the potential cause of the group of diseases, it is considered a “universal” autoimmune diet.

What Is The History Of The AIP Diet?

The Autoimmune Protocol got its beginnings in the Paleo movement when Dr. Loren Cordain (founder of the Paleo movement) first shared the concept of using dietary approaches to help manage autoimmune diseases.

This was further progressed when other members of the Paleo and functional medicine communities (with medical or research backgrounds) including Chris Kresser, Robb Wolf, and Datis Kharrazian started sharing their work on the topic.

In 2012, Dr. Sarah Ballantyne (author and founder of, began to research and experiment extensively about the protocol. Sarah’s book “The Paleo Approach” was released in January of 2014. The Autoimmune Protocol is what it is today largely due to her work.

From a small group of proponents in 2012-2014, the Autoimmune Protocol community has spread across the globe, with tens of thousands of people incorporating the protocol into their daily lives. Even doctors were starting to recommend the approach to their patients.

In 2017 the first first-ever medical study of the diet was conducted for those with IBD (inflammatory bowel disease). The results were extremely promising – with 11 of the 15 subjects in clinical remission by Week 6 of the study.

What Are The Benefits Of The AIP Diet?

As I’ve mentioned earlier, the aim of the AIP diet to reduce and manage the symptoms of autoimmune disorders.

There are many benefits surrounding this main aim, that you may experience.

Can Help Reduce Inflammation

This is one of the biggest benefits of the AIP diet. By removing specific foods from the diet, it also removes some of the reasons for the inflammation.

By reducing inflammation, the symptoms of the autoimmune conditions are also reduced, and overall health is improved.

Can Decrease Symptoms of Autoimmune Diseases

Research is still very limited in terms of the effect of the AIP diet on the symptoms of autoimmune disorders.

However, many people have reported that following the AIP diet led to a reduction in the common symptoms experienced, such as brain fog, fatigue, and chronic pain.

Restores Gut Integrity

The AIP diet is a healing, therapeutic diet aimed at healing the gut and restoring gut integrity.

Leaky Gut Syndrome occurs when toxins and bacteria are able to get through the walls of your intestine. When this happens, it can contribute to symptoms like inflammation, food sensitivities, and digestive issues.

Studies have shown that inflammation in the body can actually increase the permeability of the intestines (i.e. how easy it is for the toxins and bacteria to go through the intestinal walls).

Because the diet focuses on eliminating the foods that cause the inflammation to start with, it can help prevent leaky gut syndrome by restoring gut integrity.

Identify Foods that Trigger Symptoms

Not everyone has the same reactions to the same foods. During the reintroduction phase, you will learn which foods specifically are a trigger for you.

Boost Beneficial Gut Bacteria

Your diet can have a significant impact on the beneficial bacteria in your gut. And the bacteria in your gut plays a central role in almost every aspect of your health. Following the AIP diet helps enhance the health of your gut microbiome.

Healthy Foods that are Nutrient-Rich

The AIP diet isn’t just about removing certain foods. A big focus is on including unprocessed, nutrient-dense, anti-inflammatory foods. Vegetables form a big part of the AIP diet.

Help You Learn More About Your Body

During the reintroduction phase, you need to pay close attention to how your body reacts to certain foods. Following this diet gets you to learn more about how not only your diet – but also various lifestyle factors (more on that below) – can impact your overall health.

You’ll learn what works best for you and your needs.

Who Is The AIP Diet For?

The Autoimmune Protocol diet was developed for those who suffer from autoimmune disorders.

It is worth mentioning though, that there are certain people who – although they do suffer from an autoimmune disorder – may struggle with the AIP diet. In certain cases, these patients may need to address other issues first before attempting it.

Patients With Numerous Other Medical Conditions

The AIP diet is very restrictive, and it can get complicated if you have other medical conditions, and/or are taking medications, or if you are at risk of nutrient deficiencies.

In this case, speak to your doctor before attempting the AIP diet.

Patients Who Are At Risk Of Eating Disorders, Or Are Suffering From A Psychological Disorder

In this case, it is important to receive treatment first, then make a dietary change while still working through your treatment.

The AIP diet is difficult. It is going to potentially be an emotional and stressful experience, and it is important that you stick to it very strictly.

It is important that you will receive the emotional and psychological support you need during this process.

What If You Don’t Have An Autoimmune Disorder?

If you haven’t been diagnosed with an autoimmune disorder, the AIP diet may still be helpful. There may be certain foods causing inflammation or reactions that are affecting your health, that you may not even be aware of! (In this case, however, the Low FODMAP diet may be more beneficial to you.)

Just remember – the AIP diet is not a long-term diet. The first phase specifically is only intended to be done for up to 90 days.

Is The AIP Diet And The Paleo Diet The Same Thing?

The Autoimmune Protocol (also known as Autoimmune Paleo) was developed out of the Paleo diet.

It is essentially a much stricter diet, aimed at healing the gut.

The Paleo diet is based off how our ancestors – in the Paleolithic era – ate. The diet focuses primarily on meat, fish, vegetables, and nuts. It excludes dairy, soy, grains, and all forms of legumes.

The AIP diet takes the Paleo diet a few steps further. It also excludes nuts, seeds, eggs, and nightshade vegetables.

The aims of the two diets are different. The Paleo diet is a long-term approach focused on overall health and wellness, weight loss, and enhanced performance.

The Autoimmune Protocol is a short-term approach to reduce symptoms of autoimmune diseases and inflammation caused by it.

How Does The AIP Diet Work?

There are two phases in the AIP diet: Elimination and Reintroduction. The Elimination phase is further broken down into two stages – Transition and Maintenance.

So – if you followed the Autoimmune Protocol, it would look like this: Transition —> Maintenance —> Reintroduction

Elimination Phase Stage 1: Transition to the Autoimmune Diet

The transition stage involves switching the diet over from your current diet, to the elimination diet. The focus here is on nutrient density.

You can do the transition slowly, or all at once (i.e. go cold turkey). For most people, a gradual changeover will work best.

Elimination Phase Stage 2: Maintenance

Once you have fully transitioned to the AIP diet, you are now in the maintenance stage.

The maintenance stage needs to be a minimum of 30 days, but ideally will be 60 – 90 days.

The focus in the maintenance stage is to continue to keep the eliminated foods out of your diet while adding in very nutrient-dense foods.

By day 90, you should be experiencing quite a notable difference. If you are not getting the progress expected, it is now time to enlist the help of doctors or health care providers to determine what obstacles are causing the lack of progress with the AIP diet.

A reminder that the AIP diet is not a miracle cure, but it should have a very noticeable, positive impact on your symptoms.

Reintroduction Phase

Once you have spent 30-90 days being fully compliant in the “Maintenance” stage and experience measurable improvements, you can move on to the Reintroduction phase.

Certain foods are reintroduced, and the reactions to those foods are monitored.

At the end of the Reintroduction phase, you should have an individualized eating plan to follow that is sustainable and nutrient-dense.

You should be following a diet that is the least restrictive while giving you the best health. (It’s all about finding that sweet spot.)

The Elimination Phase: What To Eat And What Not To Eat

Foods To Eliminate During The Elimination Phase

Each of the foods in the AIP diet list below was carefully evaluated for compounds that can stimulate your immune system or harm your digestive tract. The foods that are being eliminated are ones that would contribute to an inflammatory response in your digestive, or would interfere with the healing process.

Foods to avoid:

  • All grains, pseudo-grains, and grain-like substances
  • All Dairy
  • All eggs
  • All legumes (peanuts, soy, and beans are also legumes)
  • All processed vegetable oils
  • All nuts and seeds (including seed-based spices, and don’t forget coffee and chocolate come from seeds!)
  • All fruit and berry-based spices (black pepper is a berry-based spice)
  • All nightshade vegetables, and spice from nightshade vegetables
  • All alcohol
  • All processed vegetable oils
  • All processed foods, food chemicals, and ingredients (this includes dyes, preservatives etc)
  • All refined sugars
  • All non-nutritive sweeteners

Foods To Include During The Elimination Phase

The elimination phase isn’t only about eliminating foods but also about adding in high-quality, nutrient-rich foods into your diet.

The foods listed here were selected because they are very nutrient-dense, as well as nutrient varied.

In addition to meat and vegetables, you will add to your diet:

  • Bone Broth
  • Healthy fats (think lard and olive oil)
  • Fish and shellfish (avoid if you have an allergy)
  • Organ meats
  • Colorful vegetables
  • Fermented Foods

The Reintroduction Phase: What To Eat And What Not To Eat

The reintroduction phase may take some time because you will be reintroducing foods one at a time.

There is a specific order to bring in these foods – you will start with foods that are the most nutrient-rich, and are least likely to cause a reaction. As you move down the list you get to the foods that are the least nutrient-rich and are most likely to cause a reaction.

The foods to reintroduce are:

Stage 1

  • Egg yolks
  • Legumes (the ones with edible pods only)
  • Nut and seed oils
  • Seed-based spices
  • Fruit and berry-based spices
  • Ghee

Stage 2

  • Nuts and seeds (one variety at a time, whole, nut flour, nut butter, not yet cashews and pistachios, but yes to chocolate)
  • Alcohol (in small quantities, for example, one glass of wine)
  • Egg whites
  • Butter

Stage 3

  • Coffee
  • Cashews and pistachios
  • Nightshades (specifically eggplant, paprika, and sweet peppers)
  • Cream, kefir, yogurt

Stage 4

  • Cheese, whole milk
  • Nightshades (the rest of them)
  • Alcohol (in larger quantities, for example, 2 glasses of wine)
  • White rice
  • Other gluten-free grains
  • Other legumes

You may have noticed that there are foods missing from the list above. This is because these are foods that are best avoided entirely – for example, gluten. These foods are left out due to their negative impact on autoimmune patients (like gluten), or because they have a negative impact on the health of the majority of the population (for example processed vegetable oils, refined sugars, and food chemicals and additives).

How Do I Implement The AIP Diet?

The basic approach to the AIP diet can be summarised with the 4R’s:

  • Remove all inflammatory foods, gut irritants, and toxins.
  • Replace with healthy, nutrient-dense foods and superfoods.
  • Repair with specific supplements.
  • Restore your healthy gut bacteria.

Now – I will go into more detail to show you step-by-step how to implement the AIP diet in a manageable way.

How To Transition

As I mentioned earlier, you can transition gradually, or all at once.

You may be desperate to start seeing some changes, and want to dive in head-first. However, I do want to warn you that doing a sudden transition is difficult, and may be overwhelming. If you are desperately ill, or just have the personality type that works well with going cold-turkey, then go ahead!

The gradual approach is often more sustainable but will take longer. It is a phased approach that starts with eliminating the least nutrient-dense foods (which also happen to be the most likely ones causing the symptoms).

If you follow the gradual, phased approach, it can take you anywhere from a few weeks to a few months to reach the end of the transition stage.

How To Maintain

Once you have got to the point of eliminating all the foods on the list, you have entered the maintenance stage. These 30-90 days are about learning more and getting used to your new way of eating and living.

Focus on other lifestyle factors (sleep, stress, and exercise) during this time also, so that when you get to the stage of reintroduction, you have ensured you in the best position to be aware of what foods are triggers for you.

Support during this time will invaluable for your healing. You can find groups online or in person. A certified AIP therapist will also help greatly.

How To Reintroduce

Now for the experimenting! This stage is not difficult, but it is important that you are methodical about the process.

A food journal and a symptom journal will be very helpful in this stage. Track everything. You went through all this effort to get this far, and it isn’t much more effort to make notes of everything.

Choose a time when you are not stressed to conduct the reintroduction. Being stressed, or over-tired this can affect the results of your testing, as it can cause your autoimmune disease to flare up.

What Symptoms To Take Note Of

Take note of common symptoms such as gas, diarrhea, bloating, itchy skin, rashes, and headaches.

More subtle symptoms to be aware of include joint aches, fatigue, difficulty sleeping, and mood swings.

Anything you notice that is ‘different’ to how you have been feeling over the previous few weeks – make a note. In saying that though – I also want to remind you that as humans we will go through normal fluctuations in how we are feeling from day-to-day.

In your symptom journal, keep track daily of the following:

  • Aches
  • Digestion
  • Elimination
  • Energy
  • Pains
  • Skin
  • Overall Wellbeing

You might enjoy this post on the benefits of Collagen Peptides and how they can help heal your gut.

Reintroduce Methodically

I shared with you earlier which foods to reintroduce, and in what order.

Take this process slowly. If you rush it and add to many foods at once, you run the risk of causing inflammation.

If you try a particular food and have a bad reaction to it, you may have to go back to the maintenance phase for a week or two to give your body time to heal.

This may be frustrating, but try to be patient and understanding with your body. This is very common during the reintroduction phase, as this is a “trial and error” process.

Choose Your Food

Choose one food at a time, and give a long enough break (around a week) between each new food to give your body time to recover.

Start with tiny bites

Reintroducing the food in small amounts minimizes the chance of a strong reaction. Start with half a teaspoon. Wait 15 minutes. If no reaction, then try a full teaspoon and wait 15 minutes again.

Then, if there is still no reaction, eat 1 ½ teaspoons and wait a few hours. If there is still no reaction a few hours later, you are ready to eat a normal-sized portion of the food.

Don’t eat the food again after the normal-sized portion, and watch your body for any symptoms over the next three days. Reactions can take up to 72 hours to appear.

Take note of any reactions in your symptom journal.

Did You Have A Reaction?

If you have a reaction at any stage during the reintroduction phase, then you should avoid this food in the future. Wait for your symptoms to pass before trying out the next food.

Did You Have No Reaction?

Then this food is potentially safe for you to eat.

Your next step is to eat a little of this food each day for a week, and continuously monitor your body’s responses. A reaction may not happen immediately after once-off exposure but after continuous consumption.

If you notice a reaction after eating the food daily, then you know that this is one to keep out of your diet.

Testing In The Future

Just because you are intolerant to certain foods now, it doesn’t mean that you will always be intolerant to them.

You can try reintroducing foods again at a later stage but first focus on healing your body. After about 6 months you can test the food again.

The AIP Diet And Your Lifestyle

When adopting the Autoimmune Protocol in to your daily life, there is more to consider than just the food you eat.

The management of autoimmune disease involves more than just your diet. It is important to consider these lifestyle aspects, too:

  • Sleep
  • Stress Management
  • Movement/Exercise

When it comes to healing, the combination of diet and lifestyle is very powerful. Changes to one aspect will not be as beneficial if other aspects are still causing inflammation in the body. And autoimmune disease sufferers are particularly susceptible to imbalances in these areas.

Leaky gut can be caused by a number of factors that aren’t even diet-related, which makes addressing the above points even more important. Tackle the issue from all angles to give yourself the best chance of healing.


Aside from diet, sleep is the next most important factor that will have an effect on your healing progress.

Aim for 8-9 hours per night, and try to get into bed before 10 pm to get your restorative sleep. It also helps to avoid screens for 2 hours before going to bed.

Stress Management

Stress negatively impacts your immune system. Try to avoid or reduce situations that cause you to stress – if possible.

For the situations you cannot change, you can learn to manage the stress better.

Meditation, yoga, and mindfulness are all excellent ways of reducing stress levels. You can also do an activity that you genuinely enjoy and that relaxes you such as coloring, taking a bath, or a walk outside.

Movement or Exercise

Suffering from pain can make it difficult to be active, but being inactive can actually make your symptoms worse.

You don’t need to join the local Crossfit box or start running marathons, but try to incorporate exercise or movement into your daily routine.

Take a walk outdoors, or try out yoga or pilates. These are all gentle, but effective, forms of exercise.

Are There Drawbacks Of Following The AIP Diet?

As you’ve realized already – this diet is very restrictive. It is going to be difficult to follow. It is potentially going to affect your social life. And it can be quite tedious and time-intensive – from meal planning to grocery shopping, to preparing your meals.

However, the benefits of following the AIP diet far outweigh the temporary negatives. The extreme restriction only lasts up to 90 days, and once you are in the Reintroduction phase, you will find yourself adapting to this new way of eating and grocery shopping after a while.

Katie from Wellness Mama said it best, in my opinion –
“This diet is difficult. So is pregnancy. Sometimes the best things in life require some work and denial of self. An elimination diet is temporary and it gives you a window into your own body and what you need to eat for optimal health.”

Precautions On The AIP Diet

It is important to remember that the AIP Diet is not meant to be permanent. (I repeat this phrase in various ways throughout this post because it really is so important.)

The elimination phase is too restrictive for it to be healthy in the long term. And many of the foods eliminated can provide important nutrients and healthy for you – as long as they don’t cause negative symptoms, of course.

Another point to keep in mind is that there is no one ‘perfect’ diet and lifestyle to deal with the autoimmune disease. It may take a while to find a system that works for you. What works for others may not work for you – or it may even make your symptoms worse.

Try not to compare your progress to others. As long as there is progress – then that is a good sign.

What If You Don’t Get Better On The AIP Diet?

First and foremost, if you feel like you’re having issues I always recommend that you seek the help of a Functional Medicine Doctor.

But, if you have followed the Autoimmune protocol strictly, and you don’t find your symptoms improving, you may be feeling even more confused and stressed than before.

You’ve done everything “right” – why isn’t it working?

Unfortunately, there is no clear answer. Your body is uniquely yours and if you have an autoimmune disease it can present itself in so many different ways.

Just how there isn’t one specific Autoimmune Protocol diet for everyone (in the reintroduction phase), there is no one specific answer when the diet doesn’t work.

That’s why it’s important to work with someone who can monitor your progress and what might be keeping your system inflamed.

Are your probiotics helping or hindering your progress? Is there food in the AIP diet that you are sensitive to? Do you have an undiagnosed infection (for example, a dental infection? Do you have undiagnosed anemia? Or other macro or micronutrient deficiencies?

There could be any number of reasons why you are not feeling as well as you should after following the AIP diet.

In this case, it is best to work with a certified practitioner who is experienced in the Autoimmune Protocol, who can take you through the various options and approaches, and adapt the diet to your specific needs.

This may take a long time, so it will need patience.

Both with the process and with your body (which you may not be feeling right now!) 

Don’t forget to pin this post for later!

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