Why I Switched from GAPS to Paleo AIP

Why I Switched from GAPS to Paleo AIP post image

When I started this blog I was on the GAPS diet myself and I used it in my practice when appropriate. It’s a great diet for many health conditions and I did very well on it and so did most of my patients. However, now I am intrigued by the Paleo AIP as a way to manage autoimmune diseases.

There are many conditions and symptoms that indicate a possible autoimmune condition that may be brewing. Symptoms are a way for your body to tell you that things are not right. It is always better to try to nip this in the bud before a full blown autoimmune flareup. What are these symptoms? Just to mention a few:

  • Allergies
  • Asthma
  • Digestive complaints of all kinds from diarrhea to constipation
  • Fatigue
  • Headaches and other neurological problems
  • Chronic yeast infections
  • Mood problems
  • Skin conditions
  • Blood sugar fluctuations
  • Weight issues

These complaints indicate imbalances in the gut which is part of the underlying cause for autoimmunity. See more about the cause and the triggers for autoimmunity here.

Conventional medicine still tells us that there is no known cause for autoimmunity. That is simply not true. It’s all in the scientific literature that is thoroughly documented in The Paleo Approach.


Both diets are elimination diets and very restrictive. GAPS eliminates not only grains and legumes, but also starchy foods like non-gluten grains, potatoes and some starchy roots. The GAPS Intro diet also eliminates all dairy, nuts and many other foods (see the Intro stages here). You move through the stages and slowly add in one food at a time to make sure you can tolerate it until you are on the full GAPS diet.

In my practice I would usually start a person on full GAPS, especially if they were new to eating real food. The Intro diet is so restrictive a person would be starving on it and freaking out about each meal. The full GAPS diet is hard enough for a newbie so I would start there in order to slowly allow them to learn how to manage the diet. We would move into the Intro when they were ready with all the new foods they had to make at home. This took a few weeks for some – for others a few months.

Once a person learns all the recipes they like it becomes second nature to organizing shopping and cooking. I love the fact that the GAPS diet is taken from the SCD and tweaked up to the level of the Weston Price Foundation recommendations. It’s all about eating real, unprocessed foods and certain super foods that are truly super foods like organ meats and fermented foods – not the weird, expensive so-called super foods that change each month.

Many people have gotten great results from the SCD or GAPS diets. Some people get results but then unfortunately seem to experience symptoms again. Others are on the diet for much longer periods of time than recommended. Dr. Campbell-McBride (GAPS) advises to be on the diet up to two years and then to introduce foods back in (or sooner if symptoms allow).

I loved being on GAPS and as you know from reading this blog, I have tons of GAPS and SCD legal recipes. I also followed the Paleo diet recommendations as these were in line with Weston Price and GAPS and is grain and dairy free. I would have stayed on GAPS forever except for one thing…

Resistant Starch

When I started to read about resistant starch (find out more about why I added resistant starch to my diet here) and how it feeds the gut bacteria, my first instinct was to reject it because the whole premise of the SCD and GAPS diets is to starve out the pathogenic bacteria. However, in discussions with others passionate about gut health, I realized that there comes a time when starving the gut bacteria is no longer necessary and if continued may actually be detrimental.

In my experience, those who are on the diet for years, risk the health of their microbiome. Unless they can tolerate eating lots of probiotic foods and supplementing daily with probiotics, they are still starving all the bacteria – bad or good. I wondered if some of my residual issues may be because I was not actively feeding my gut bacteria.

It became a much larger question in my mind when one of my patients who had been on GAPS for years become very ill with a c. diff infection. She had been managing her Crohn’s disease quite well on the diet and then suddenly went into a flare that turned out to be c. diff.

She had not been exposed to it in a hospital setting or in any other way that we knew of. The conclusion we came to was that she was lacking enough beneficial bacteria to balance the c. diff.

A Lesson Learned

We know that our ancestors ate 50 – 200 gms of fiber a day. That is up to ten times more than most people eat today. It’s all about getting enough fiber that ferments in the colon. The SCD and GAPS diets try to minimize fermentation in the colon.

When you don’t eat enough dietary fiber, the microbes are forced to consume the mucous membrane! This has the potential of being disastrous which is what happened to my patient! Not only do you miss out on the beneficial byproducts of fermented fibers, it can also become inflammatory to the mucous membrane and potentially cause damage and allow the pathogens to emerge.

We immediately added resistant starch into her diet in the way of plantains, which were well tolerated. We also added sweet potatoes as these have different fibers and are part of the Paleo diet. This was also well tolerated. She plans to add other starches slowly but will adhere to the AIP Paleo diet, so, no white potato.

She has recovered well from the c.diff and is thoroughly enjoying the new foods. As part of the recovery plan she had a lot of bone broth, gelatin in coconut puddings and, importantly, started to eat organs in the way of chicken liver pate.

She is also taking a buyrate producing bacteria from Japan that seems to be working.

I believe this has helped her recover from a very serious illness.

My Transition to AIP

Paleo AIP was developed by Sarah Ballantyne PhD as a way to manage her autoimmune issues.

This diet emphasizes removal of any chemicals additives and packaged foods for real, high quality (grassfed) animal products. The initial 30 days of the AIP is the hardest elimination diet as it eliminates grains, dairy, eggs, legumes, nightshade vegetables, nuts and seeds and the spices that comes from seeds.

However, after a month you start to slowly, one food at a time, add in each food and see how you tolerate it. It’s a process and may take a short amount of time or months. Some foods you may never tolerate and this is the best way to find that out.

On the other hand, you are allowed some starches that are not allowed on GAPS and that is wonderful.

It really wasn’t hard to add some new foods in, such as sweet potato (a safe starch) and plantains, as long as you eat a little at a time and go slowly. Eliminating nightshades was not hard, as I do not like most of them – only tomatoes will be missed. Nuts are harder to forget but I can still use coconut flour for baking. I am planning to experiment with using arrowroot flour and tigernut flour as well.

Eliminating some of the seed spices will probably be difficult but worth a try. As Sarah Ballantyne says in her book The Paleo Approach, after a while a person can experiment with adding in the various spices to see if they can tolerate them. I plan to do that.

As with all diets, one must follow them at first and then tweak them to make them manageable in your life and to your tolerance. There is no reason to stay off of certain foods if you do not have a problem with them. Trial and elimination is the best way to determine which foods you can tolerate.

I’m excited about this new diet and happy to be eating some starches again!

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Leave a Comment

  • maartje August 5, 2016, 1:54 pm

    How are you now?
    I was wondering, on the GAPS diet you have toe eat many eggs, but on AIP they are not allowed!
    Wat are you doing with eggs?