Autoimmune Protocol, 101

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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.

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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 damage our bodies. It can be helpful for all types of autoimmune (or inflammatory) issues.

What is Autoimmunity?

Autoimmunity is essentially where your body does not know the difference between the good and bad cells in your body. Instead of being a pacifist and letting the good guys stay, your body decides to try and make everyone get out and starts attacking.  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.

What is The Autoimmune Protocol?

The Autoimmune Protocol is a way of eating that helps to calm your body and helps the healing process begin. Sounds pretty good to me.

It does this 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 it cannot be completely cured, autoimmune disease can be put into remission.

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 IN 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 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!

The “Yes” AIP Foods

EAT ALL THE VEGGIES! (well, mostly) 

Colorful veggies
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)

Liver, kidney, heart, etc.


Wild caught is best, but if farmed is all you can do, that’s better than nothing!

Quality Meat

Grass fed, pasture- rasied is better, but again, 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.

The “No” AIP Foods

On top of eliminating what the Paleo lifestyle does, AIP also eliminates:





      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 does “Strict” AIP last?

Well, that’s a great question. The recommended amount of time is at least 30 days- 3 months, after that it’s up to you and your journey. Some people only need the beginning recommended time, 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 (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 😉

As always, if you have any questions, or are interested in starting this journey for yourself and need assistance, don’t hesitate to contact me through the work with me page. We can jump on a call and figure out what would be best for you! 

And if you’d like to receive my emails, where I send out additional bi-weekly insights, sign up here —>

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  1. Victoria Kircher says:

    Hello, I enjoyed reading ur MS story. I myself have MS for almost 40 yrs. May I suggest another another exercise for you…when I was diagnosed back in 1981, in Balto., Md@ John’s Hopkins my Neurologist Benjamin Brooks M.D., told me that the best exercise for MS is swimming!
    I did not take his advise @ first but after having another attack where my arms & hands were numb for a month.
    Then I joined a gym that had an indoor & outdoor pool. That was it! It took some time getting adjusted to the water, but the water was very comforting to my soul, brain & muscles. Don’t have to worry about getting overheated while swimming. I didn’t like getting my hair wet though. So I took a deep water jogging class. That was it! I loved it! You are exercising ur arms & legs stomach & not getting chlorine in ur hair! I just wanted to suggest this. Maybe you would like to try it. I am in the SPMS stage now, I was on Copaxone I injs for years, but my Neuro switched me to Gilenya for now. I use a Rollator now to help with balance issues. I did enjoy reading ur story. My best to you!
    Give the pool a try, u may like it. Stay away from the warm therapeutic pools also…My Best to you, Vicki

    • LissMS says:

      Thanks for the suggestion! I haven’t been swimming in ages! I used to love it when I was younger, so I bet I would now. It would be a nice, cool activity to add to my list. And it sneaks up on you too! Best to you as well! <3

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