Auto Immune Protocol (AIP) Diet – A Basic Guide

For those of you who are regular visitors to my blog you will know that I recently embarked on something called The Gut Health Protocol (TGHP), tweaking my currently paleo/ ketogenic diet to an Auto Immune Protocol (AIP)and Low Fermentable Oligo-saccharides, Di-saccharides and Mono-saccharides & Polys diet or low FODMAP’s for short! (Yes, it’s a bit of a mouthful!!)
The protocol I am following is to treat my Small Intestine Bacterial Overgrowth (SIBO) which is an imbalance in the bacteria and types of bacteria in the gut. If you haven’t already taken a look, you can read my article about it here.
TGHP is a basic protocol that is the same for everyone, then you add in and/or tweak certain areas of it to work around your symptoms of SIBO and any other health conditions that you may have. As I have been following the paleo diet for three years now and am still suffering with a range of issues, one of the add-ons that is suggested for those with auto immune conditions, is adapting to an Auto Immune Protocol diet.

What is Autoimmune disease?

It is suggested that there are over 80 different kinds of auto immune diseases and they can affect any part of the body. They tend to be characterised by an under or over active immune system. With an over active system the body may begin producing antibodies that instead of fighting infections, attack the body’s own tissues, (Auto Immune Disease) decreasing the immune system’s ability to fight invaders. The trigger is often unknown but they all lead to chronic inflammation and tissue damage.
There is no cure for auto immune diseases but treatment focuses on reducing immune system activity. Dr Sarah Ballantyne A.K.A ‘The Paleo Mom’ has published a number of books on AIP and states that although there is no cure, you can put an AI disease into remission using the right type of diet and supplementing where needed. The differences in conditions are the areas / organs that are impacted on.

To give you an example, the first three AI conditions will be explained very briefly.

Types of auto immune diseases include:
• Rheumatoid arthritis – this impact’s on the joints in the body. Antibodies produced by the immune system attach to the linings of joints. Cells from the immune system can then attack the joints causing swelling, inflammation and pain.
• Multiple Sclerosis (MS) – The immune system attacks nerve cells causing symptoms such as pain, weakness, and poor coordination and muscle spasms.
• Psoriasis – is an overactive immune system where blood cells (called T-cells) collect in the skin. The over activity stimulates skin cells to reproduce more rapidly producing silvery scaly plaques on the skin.

• Lupus
• Inflammatory bowel disease (IBD)
• Type 1 Diabetes mellitus
• Graves’ disease.
• Hashimoto’s thyroiditis
• Myasthenia gravis
• Vasculitis
• Coeliac
• Alopecia

Depending on what website you read depends on whether Chronic Fatigue Syndrome (CFS) and Fibromyalgia are considered auto immune diseases. Some medical sites will suggest that they are not, even though they display many of the symptoms of an AI disease. New research suggests that a condition known as leaky gut (tiny holes in your gut wall) is responsible for all auto immune diseases. Leaky gut has been linked to both Chronic Fatigue Syndrome and Fibromyalgia so it’s possible that following an AIP diet could help reduce the symptoms of these two conditions.

Leaky Gut

The gut wall has been found to produce a chemical knows as zonulin which helps the gut to moderate its environment. Usually the gut wall remains closed and only small molecules such as nutrients are able to pass though the gut lining and into the body. Occasionally the gut wall will open in order to flush out unwanted invaders such as infection in the intestines. However if the cell wall produces too much zonulin, then the gut wall can remain open for some time. This can allow food, bacteria and other debris from your intestines to leak into your body, causing inflammation; this is what’s known as ‘leaky gut’. If the issue isn’t fixed then it becomes chronic and triggers disease. Research suggests that anti- nutrient foods such as grains, gluten and legumes are possible triggers for leaky gut as well as imbalances in the gut bacteria (known as gut dysbiosis).

How AIP works

AIP is a form of elimination diet which looks to remove certain foods and food groups that are known to aggravate the gut, cause inflammation, gut dysbiosis and activate the immune system. The AIP diet is very nutrient dense so although you may be cutting out a wide range of foods, you don’t have to worry that you won’t be getting enough nutrients.

By removing certain food groups for a period of time it helps to reduce inflammation in the gut allowing it to heal and symptoms to reduce/ clear. Once a person is feeling well and has had no flare ups, many of the foods that have been avoided are slowly (VERY slowly and one by one) reintroduced. Patients are encouraged to keep a food diary when reintroducing foods and only introduce one food item every 5 days. When a food item is added back into the diet you should allow 72 hours for any symptoms to arise as this is how long it can take for Auto Immune (AI) symptoms to flare up if the food is causing issues. If a food item doesn’t cause any issues then it is safe to add back into the diet, but for the foods that cause any symptoms to return, they are best avoided completely. Some people may find that they can tolerate small doses of certain foods but larger amounts might cause issues. By keeping a food diary and monitoring the amounts when reintroduced this can help you work out the amounts you can tolerate.

Ideally there are certain food groups that you should continue to avoid to prevent relapsing / causing your condition to flare up again. Foods that are heavily processed and contain a lot of artificial flavours and colourings, foods that are extremely artificial, products that contain lots of sugar, grains, gluten and certain beans and legumes. It also helps to eat food that is of the best quality such as organic grass fed meats, line caught fish, free range eggs, organic vegetables and fruit and any other ingredients sourced organically. The reason for this is because organic ingredients won’t have been treated with pesticides or chemical fertilisers; animal products won’t have been treated with antibiotic drugs or fed artificial food. An ingredient that is organic tends to be more ethically sourced too. Over all it means that the food you eat won’t be filling your body full of ‘nasties’, which means your gut doesn’t get damaged and your body isn’t filled with unnatural chemicals!

Going AIP

If you are familiar with the paleo diet then you will already be familiar with what kinds of foods that are and aren’t allowed (as well as the reasons for avoiding them!). However if you are new to paleo then it may be a little bit overwhelming as there will be a lot of adaptions to make such as foods to avoid, foods to introduce, how to use these new and possibly unfamiliar ingredients, tips for living your life this way and tips for being organised.

In short the autoimmune protocol avoids ingredients that aggravate the gut such as grains, legumes, beans, nightshades (which will be explained below), dairy, eggs, nuts, seeds, foods that contain unnatural (artificial) chemicals and additives. I will give links to the ‘yes – no’ lists so that you can have a look at the full list of ingredients.

*Nightshades or ‘the Solanaceae’ are a family of flowering plants ranging from annual and perennial herbs to vines, shrubs, trees, agricultural crops, spices, weeds and medicinal plants. Many of these contain alkaloids and some are even highly toxic! They commonly include collected and cultivated species including the potato (white), tomatoes, aubergine (eggplant), capsicum including bell peppers and chillies, paprika, pimentos, cape gooseberry and goji berries. The whole list can be found on the Paleo Mom’s page. It also includes other items that are not food such as ashwagandha (ginseng) and tobacco!

As well as removing foods you will be adding in things that you may not be familiar with such as bone broth, organ meats, foods that are fermented / probiotic as well as the more ‘normal’ things such as high quality meat and fish, organic fruit and vegetables.
If you are considering going AIP then you need to allow yourself about a week to do some planning, buying in foods so that you are prepared, maybe batch cooking a meal or two and printing off the ‘yes’ ‘no’ lists so that you are familiar with the things you can and can’t have.

First of all I recommend doing a bit of reading; The blogs below are ones that I have found particularly useful but you can do a google search and there will be more than enough websites for you to choose from. I currently only have one AIP cookbook as it was what I bought when I first decided to go paleo. At the moment I also have to follow a Low FODMAPs diet, meaning my diet is even more restricted so AIP cook books offer me limited recipes. However, if you are only following AIP then the following books might be worth purchasing based on what I have heard about them.

Blogs to read

Autoimmune Paleo
AIP lifestyle
The Paleo Mom
Phoenix Helix
Paleo Cajun Lady

Books to buy

  • The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol – Angie Alt
  • The Paleo Approach: Reverse Autoimmune Disease and Heal Your body (not a cookbook) AND The Paleo Approach Cookbook: A
  • Detailed Guide to Heal Your Body and Nourish Your Soul – Sara Ballantyne
  • The Autoimmune Paleo Cookbook Hardcover – Mickey Trescott
  • The Healing Kitchen: 175 + Quick and Easy Paleo Recipes to Help You Thrive Paperback – Alaena Harber, Sarah Ballantyne
  • Seven Steps to AIP


Before you embark on the AIP diet, its best to set a start date and stick to it! Give yourself the time to prepare and you will find it easier to stick with.
Step One – print out a list of the yes/ no ingredients and keep them in the kitchen for quick reference. It’s also handy to save the yes-no list as a book mark on your computer and on your mobile phone if you have one. That way if you are online shopping or out in a store, you can quickly reference the items you can and can’t have. If internet signal is an issue you can always screen shot or photograph a copy of both lists so that you can call it up when you need it. For those without a mobile try the old fashioned way of keeping a written list in your bag or wallet.
Step Two – find a few recipes that you feel confident to try; ideally stick to recipes that you may be familiar with such as family classics – Bolognese, roast chicken/meat dinner with veg, meatballs, cottage pie those sorts of things then find an AIP version. Once you have a handful of recipes write down the ingredients that you’ll need to make them.
Step Three – Do a food shop! Once you have found the recipes you want to make its time to source the ingredients. In the UK online shops tend to have more variety than going into the stores and sometimes it’s cheaper to buy some ingredients in bulk (such as seasoning, meat and cooking oils). If you don’t work weekends then it would be a good idea to plan to get your food shop on a Friday and then spend the weekend organising your fridge and cooking meals.
Step Four – Cooking/ preparing your meals; Batch cooking is the best way to get ahead with the AIP diet and it makes it so much easier to stay on track. Make up a big pot of a recipe so that when you come to start the diet you have some meals already made up. You could make a batch of cottage pie, cut into portions and freeze some so that you have them for another time (just remember to write the name/ date on them). Soups and stews are also really easy to make especially if you have a slow cooker. If you don’t own a slow cooker it’s really worth investing in one as it will make your life so much easier. Soups and stews can be left cooking while you are at work and are ready to serve the moment you walk through the door!
Tip –when batch cooking for the first time, you want to have 2-3 recipes made so that you have a lunch and an evening meal for the first three days as they will probably be the hardest. Breakfasts are usually the trickiest as you are limited to what you can take with you on the go. Some pancake recipes can be made the day before and kept in the fridge, or you can pre-cook meat (slices of ham, homemade sausages or patties) and serve with some sauerkraut (fermented veggies that are naturally probiotic) and olives, or some homemade coconut milk kefir (probiotic yogurt) with some fresh fruit.
Step Five – You are ready to start eating AIP! To ensure you stay on track plan out the foods you plan to eat for the first week. Draw up a table if you need to, tab the pages of the cook books / print out the recipes and make sure you have everything you need.
Step Six – Keep a diary; it’s easy to forget all the symptoms that you are suffering, especially once you start to improve so by keeping a diary it helps you to really see how much you are improving (or if not, clues as to why not could be in the diary).
Step Seven – Keep planning ahead; continue to look for recipes to try because as you become more familiar with this way of eating, you will become more confident at working with the ingredients. If you are not sure how to use a certain ingredient or want tips on how to utilise it then YouTube is a good place to start! Just type in the ingredient or try ‘autoimmune protocol’ and the ingredient and you should get some tips, recipes and information on it.

Yes-No lists

Below are a few websites that have a good list of yes and no foods. Sometimes you will find conflicting information, but as a rule of thumb I tend to check out ‘The Paleo Mom’ first as Sarah Ballantyne is the leading woman for autoimmune and has written a few books about the subject! It’s entirely up to you what information you decide to go with but just remember to note down if any foods give you issues – especially if they are foods that are a grey area! (Maybe foods – see The Paleo Mom link).
• The Paleo Mom –
• Paleo Cajun Lady –
• Ultimate Paleo Guide –
• Phoenix Helix –


Finally I want to mention FODMAPs because the subject tends to get mentioned a lot in the AIP and it is closely linked to autoimmune disease. It’s basically another form of elimination diet that people follow to help with certain gut issues (such as SIBO – for more details see my last article). It focuses on removing food groups that are types of sugars that the body finds hard to digest. The types of sugars are broken down into sub groups – fructose, lactose, sugar polyols, fructans and galacto-oligosaccharides (GOS). These sugars are found in fruits (fructose), milk (lactose), sorbitol which is often used to sweeten foods (sugar polyols), onions and garlic (fructans) and legumes such as baked beans (GOS). Some of these foods will be on the AIP ‘yes’ list but a person who is also following a Low FODMAPs diet will have to also eliminate these foods too.

A low FODMAPs diet is recommended to those who suffer with Irritable Bowel Syndrome (IBS), but it can be recommended to anyone who is suffering from the symptoms of IBS list (below). Ideally you would want to speak with your doctor first if you are having serious gut issues, so that they can rule out any other causes.
Like the AIP diet you follow a low FODMAPs diet for a period of time (until the gut has improved) before reintroducing foods. As foods are reintroduced a person should keep a diary so that they can monitor any symptoms. With FODMAPs you may react to larger amounts of some foods but be able to eat them in much smaller doses. Some people find that they tend to react more to some of the sugar sub groups than others. For example they may not be able to eat any of the foods in the fructans and GOS group, but they may be able to tolerate sugar polyols, fructose and lactose. Foods that are an issue should be avoided completely as they will only continue to aggravate the gut and flare symptoms.


IBS is a long term condition of the digestive system that is thought to be related to increased sensitivity in the gut and problems with food digestion. Symptoms can differ from person to person as can the severity. It tends to first develop in people between the ages of 20 – 30 years old, affecting twice as many women as it does men. There is no cure although medication can be used to help with the pain and discomfort. Patients of IBS are encouraged to reduce the amount of fibre in their diet, take regular exercise, reduce stress and identify foods that trigger their symptoms!

Symptoms Include;
• abdominal (stomach) pain and cramping, which may be relieved by having a bowel movement
• Occasionally experiencing an urgent need to go to the toilet
• Feeling like you haven’t fully emptied your bowels after going to the toilet
• Bloating and swelling of the stomach
• Passing mucus
• Excessive wind (flatulence)
• Diarrhoea
• Constipation
Additional Issues such as
• Lethargy (lack of energy)
• Feeling sick
• Back ache
• Bladder problems such as waking in the night and needing to urinate; difficulty emptying the bladder, in server cases incontinence
• Pain during sex (Dyspareunia)
• Some people may suffer depression and / or anxiety


Dr Sara Gottfried MD – Is the autoimmune protocol necessary-
Dr Chris Kresser –
Fasano, A., 2Sonulin, regulation of tight junctions, and autoimmune disease,” Annals of the New York Academy of Sciences1258 (2012) : 25-33 –
NHS; Irritable Bowel Syndrome –
Office on Women’s Heath; Auto Immune Diseases Fact Sheet-
The Paleo Mom; The auto immune protocol –
The Alternative Daily; Leaky gut causing chronic fatigue –
University Health News; 5 top reasons you might have leaky gut syndrome and feel tired all the time or have depression symptoms-


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