The Autoimmune Protocol, an Overview.

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I'm Alissa!

I help women who have also been diagnosed with Multiple Sclerosis make specific and personalized diet, lifestyle & subconscious changes so that they can begin to heal their body, reduce disease symptoms, and return to a life they love.

hey there,

This is the first in a series of posts about the Autoimmune protocol. Enjoy!


The Autoimmune Protocol, Autoimmune Paleo or simply known to most as AIP, is a type of elimination diet that helps heal the immune system, when it has gone rogue and started to hurt our own bodies. It can be helpful for all types of autoimmune (or inflammatory) issues.

Autoimmunity is where your body does not know the difference between the good and bad cells in your body. Your immune system gets a little confused and decides to try and make everyone get out and starts attacking all cells, instead of just the invaders.  This can be going on for a long time before developing into a full blow autoimmune disease.  Shockingly enough, there are more than 80 (!) types of autoimmune diseases, many of them are conditions that we grew up thinking were somewhat ‘normal’ or ‘routine’. Any system of your body can be affected by autoimmunity, from your brain, to nervous system to glands and even skin.

So what is this ‘Autoimmune Protocol’ anyway?

The Autoimmune Protocol is a way of eating that helps to calm your body down and begin to heal itself.

Sounds pretty good to me.

The Autoimmune Protocol works by reducing inflammation around the body, and most importantly, the gut. Many foods that we have eaten over the years have been damaging to our gastrointestinal (GI) system and have been inflammatory to our bodies. AIP is an elimination diet that targets these inflammatory foods, removing them from our daily lives and puts our GI tract on a path to healing itself. Although they cannot be completely cured, autoimmune diseases can be put into remission with this approach.

This is not just an elimination diet however. Yes, many things are eliminated, at first. But one of the main points of AIP is to concentrate on adding the most nutrient dense foods available. Unfortunately the Standard American Diet (SAD), is fairly nutrient deficient, and nutrient deficiency is a key factor in developing autoimmunity. Adding in nutrient dense foods helps to jump start the autoimmunity healing process. Eating nutrient dense foods will help reduce inflammation, restore proper gut microorganisms and help heal the gut. It will also help balance hormones and regulate the immune system.

But the AIP lifestyle doesn’t stop there, it’s called a lifestyle for a reason! There are several other components of the AIP that are equally as important to healing as the food we eat. Managing stress, prioritizing sleep, avoiding environmental toxins and getting plenty of movement are all essential components of AIP as well. If these other aspects are ignored, you may not see the results you are looking for with diet alone! More on these topics in later posts 😉

SO, WHAT FOODS CAN I HAVE IN THE AIP WORLD?? Let’s start there, shall we?

EAT ALL THE VEGGIES! (well, mostly) 8-14 cups a day

  • Colorful veggies, eat the rainbow!
  • Green veggies
  • Cruciferous veggies (broccoli, cabbage, kale, turnip, cauliflower, arugula, watercress, brussels sprouts etc)
  • Sea veggies (except chlorella and spirulina)

Organ meat and Offal (offal ain’t awful) 4 servings a week

  • Liver, kidney, heart etc.

Seafood at least 3 times a week

  • Wild caught is best

Quality Meat

  • Grass fed, pasture raised is better, but if you can’t swing it, it’s ok!

Quality Fats

  • Olive, avocado, coconut and palm.


  • Fruits are meant to be kept in moderation, lower than 20g of fructose daily.

Probiotic Foods

  • Fermented veggies/fruit, kombucha, kefir, coconut milk kefir, coconut milk yogurt. (however, if you react to yeast, as I do, these foods will be an issue for you!)

Glycine-rich Food

  • Foods that contain connective tissues, joints or skin, such as organ meat and bone broth.


(pun intended) AIP eliminates:





Processed Vegetable Oils/Processed Food Chemicals

Added Sugars/Sugar Alcohols 





  • Potatoes, tomatoes, eggplants, sweet/hot peppers (and their spices), cayenne, tomatillos, goji berries, hot peppers and all spices derived from peppers, like paprika etc.

Potential gluten-cross reactive foods


NSAIDS (this one is really hard for me with migraines) and Birth Control

Non-nutritive sweeteners

Emulsifiers, thickeners and food additives

This seems like a lot of things, at least it did to me when I first looked at the list, especially the nightshades! I lived off of tomatoes for the first 25 years of my life! But once I got into actually cooking AIP recipes, I found that it wasn’t that bad and it was actually quite good! I got excited to experiment and find new ways of making old tastes. Also, once I realized the reasons WHY these foods were eliminated, they became much easier to get rid of.

There are many reasons to eliminate these foods at first. They all harm our bodies in some way most creating gut irritation or dysbiosis, creating gut permeability (leaky gut) or causing inflammation. That’s all reason enough for me!

How long do I have to stay Strict AIP?

Well, that’s a great question. The recommended amount of time is at least 3 months, after that it’s up to you and your journey. Some people only need 3 months to notice improvements, then they can begin to re-introduce foods. Some people need much longer, which can be up to a year or more.

So how do you know? It all depends on how you feel. Your initial symptoms should be gone (or mostly gone), you should be generally feeling better day to day. Listening to your body is key during this process. Keeping a journal of symptoms is a great way to go about this so you can look back and see the big things, but also the little things that you may forget. Once you are ready for re-introductions, there is a way to best go about those as well, which is another post! So keep on the look out for that as well 😉

The one major thing to remember when starting on an AIP journey is the elimination phase is not meant to be forever. It is meant to be a healing time, where your body is able to reset itself.  Which may take a few months for one person and over a year for another. You’re walking your own journey, and no one else’s.


As always, if you have any questions, don’t hesitate to contact me through the ‘work with me’ page, and I’ll get right back to you!

And if you’d like to join the LissMS Community, sign up here!

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