The WHYs behind the Autoimmune Protocol: Nuts and Seeds

September 4, 2012 in Categories: by

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When it comes to understanding the whys behind the extra restrictions of the autoimmune protocol, it is usually easy to see the link between certain foods and increased intestinal permeability and/or interaction with the immune system.  In the case of nuts and seeds, however, it is actually much harder to make a very strong case for their removal from the diet for those with autoimmune conditions.

There are plenty of books and websites that list all nuts and seeds as foods to avoid on the paleo Autoimmune Protocol (for example, The Paleo Solution, It Starts With Food, and Practical Paleo).  The rationale ranges from none to a simple statement that nuts contain lectins and phytic acid.  However, as I have delved deeper into this subject, the science behind this argument is lacking.

It’s not about lectins.  As I have mentioned before, lectins are a class of sugar-binding proteins with a variety of functions in both plants and animals.  Almost every food contains lectins and this fact by itself is not sufficient to avoid eating something (otherwise we wouldn’t eat anything!).  The lectins that we avoid eating on a paleo diet are lectins such as gluten (and related lectins in other grains and legumes) that are known to survive cooking, be poorly digested, interact with the cells that line the gut, increase intestinal permeability and/or cross the intestinal barrier largely intact where they can stimulate the immune system.  To date, there is no scientific evidence that the lectins in nuts and seeds cross an intact gut barrier or prime the immune system.

It’s not about phytic acid (well, not much, anyway).  Nuts are relatively high in phytate, which is the salt of phytic acid, i.e., it is phytic acid bound to a mineral.  These minerals are not available for absorption, which is why consuming large amount of foods high in phytic acid and/or phytate is not a good idea (it leads to mineral deficiency).  And it certainly means that the minerals found in nuts are not really a good rationale for eating nuts, if we can’t absorb them very well (although I should mention that your gut microflora help release the minerals for you to absorb).  Consumption of excessive phytic acid/phytate may irritate the lining of the gut and contribute to a leaky gut by reducing the activity of a variety of digestive enzymes, including trypsin 1, pepsin 2, amylase and glucosidase 3.  However, phytate may also be an important antioxidant and help reduce cardiovascular risk factors and risk of developing cancer when consumed in moderate quantities 4Dose is important here.  But, this is an argument to limit nut consumption, not cut nuts out of our diets completely.

It isn’t about the omega-6 content of nuts.  Nuts tend to have much more omega-6 polyunsaturated fats than omega-3 polyunsaturated fats.  So, when one of the main goals of a paleo diet is to normalize the ratio of omega-3 to omega-6 fatty acid intake, eating large quantities of nuts is not helpful.  With the importance of resolving inflammation for those with autoimmune condition, increasing the amount of omega-3 fatty acids (and simultaneously decreasing omega-6 fatty acids) in the diet is critical.  Even walnuts, which have the highest omega-3 content of all nuts have a 1:3 ratio of omega-3 to omega-6, and these omega-3 fats are the short chain ALA fats which are not as readily used by the body as the longer chain DHA and EPA that are found in seafood and grass-fed meat.  Macadamias are the exception with the vast majority of their fat being monounsaturated.  However, in a diet rich in fish and grass-fed meat, small quantities of nuts that are conscientiously consumed should not be a problem.

So, why are nuts so uniformly restricted on the paleo autoimmune protocol?  Actually, they aren’t.  Two prominent examples are the opinions of Prof. Loren Cordain, author of The Paleo Diet and The Paleo Answer, and Dr. Terry Wahl’s, author of Food As Medicine and Minding My Mitochondria and well-known for her TedX-Iowa Talk.  Prof. Loren Cordain hesitantly recommends their removal for those with autoimmune disease with the following caveat:  “In addition to peanuts, which are not a nut at all, but a legume, tree nuts (almonds, walnuts, pecans, brazil nuts etc) are one of the most common allergenic foods.  To date, tree nuts have been poorly studied for antinutrient content, and it is unclear if they increase intestinal permeability of adversely affect the immune system.  This would be one of the last foods I suggest restricting [for those with autoimmune disease].” 5.  Dr. Terry Wahl’s lumps nuts in with grass-fed dairy and thoroughly-cooked sprouted legumes as foods she consumes “very little” of but doesn’t restrict altogether 6.

It boils down to two simple facts.  Tree nuts are one of the top allergens and most common food sensitivities.  People with autoimmune disease are very likely to have a leaky gut, which increases their susceptibility to developing food allergies and food sensitivities (the difference is in the type of antibody formed).  This means that people with autoimmune disease are more likely to have a sensitivity or allergy to nuts (and seeds) than other people.  And cutting nuts out of the diet using an elimination diet approach such as the autoimmune protocol is a good way to isolate whether or not nuts are a problem for you.  If you continue to eat something that you have an allergy or sensitivity to, it is very difficult for your gut to heal and for your immune system to deactivate. 

 Additionally, the fiber in nuts and seeds can be difficult to digest, particularly almonds, pistachios and hazelnuts (read my FODMAP post), which is an additional way that some people can be sensitive to them.

I personally have found that avoiding almonds has been very important for me although I seem to be able to handle small amounts (like 1-2 ounces) of other nuts (typically macadamias, walnuts and pecans).  Larger amounts of nuts do seem to be a problem for me and I attribute this to the omega-6 contribution that they make to my diet.  I still think it’s important to remove nuts and seeds from your diet, at least for a month, when you first start the autoimmune protocol.  However, unlike tomatoes or egg whites, which have a much higher ability to be problematic, reintroduction of individual nuts and seeds should only worsen your symptoms if you have a sensitivity.



1 Singh M and Krikorian AD “Inhibition of trypsin activity in vitro by phytate” J. Agric. Food Chem., 1982, 30 (4), pp 799–800

2 Vaintraub IA and Bulmaga VP.“Effect of phytate on the in vitro activity of digestive proteinases” J. Agric. Food Chem., 1991, 39 (5), pp 859–861

3 Kunyanga CN et al “Antioxidant and type 2 diabetes related functional properties of phytic acid extract from Kenyan local food ingredients: effects of traditional processing methods.” Ecol Food Nutr. 2011 Sep-Oct;50(5):452-71.

4 Food Phytates; N.R. Reddy and S.K. Sathe, editors. 2002



You said “To date, there is no scientific evidence that the lectins in nuts and seeds cross an intact gut barrier or prime the immune system”

What then, is the specific evidence that the lectins in grains cross an intact gut barrier or prime the immune system?

i can eliminate them for at least a month. I suspect I do not have a problem with most nuts. But, I’m wondering how almond Milk and cashew milk fit in? I love them, & feel they are a good substitute for dairy in recipes. I probably consume one serving per day. Thoughts?

If I’ve done the ELISA food sensitivity test, does this mean I can stop the AIP and go back to regular paleo? None of the AIP flagged foods were positive for me.

I was wondering why nuts and seeds are not allowed in autoimmune paleo but you can still eat fruit that contain seeds. What is the difference between for example a watermelon seed and a sesame seed?

This topic came up on the Facebook page and I am really interested to know the answer. What about the seeds in berries? I have been doing AIP for 3 weeks and was so happy to reintroduce seeds first after 30 days. However I have been using berries in my smoothies (strawberries, blackberries, and blueberries) which all include seeds. Do I have to start over again?! I hope not. Please let me know so I know what step to take next.

Hello Paleo Mom, first can I say thank you. Thank you for the time and dedication that you have invested in this field. You are paving the way for so many of us. When I was 13 I was diagnosed with Juvenille Rheumatoid Arthritis. I’ve had ups and downs. On meds, off meds. It’s been a roller coaster. I have been trying to manage my swelling (my left knee swells up when not on meds) through diet for the past 4 months. I did a 21 day Cleanse (Alejandro Junger) and then amped it up anotch with the Myer’s Way (Amy Myers). Both Junger and Myers maintain that 100% Cacao (NOT cocoa) is okay on the the Autoimmune Protocol but I’ve read from some others that cacao is NOT okay. What are your findings/opinion on the matter? I highly regard what you have to say due to your research-based approach. Your response would be appreciated. Thank you.

For arthritis forget supplements. Stop ingesting the causes, lectins. Arthritis-causing lectins are in grassy grains (wheat, barley, rye and oats), in legumes (beans, peas and peanuts), and in nightshades (potatoes, tomatoes and peppers). Aggravating the arthritic condition is fructose. Fructose is in any food which tastes sweet. The combination of fructose and any of the above foods opens intestine tight junctions and allows them into the bloodstream.

Get your nutrients from meat and fat …..especially fat.

Almonds in the United States are irradiated which is a problem for our liver as our liver can’t handle very well irradiated nuts. Both organic and inorganic almonds are irradiated. Most all other countries don’t irradiate almonds

Hi Sarah
I have Graves, and have been following the AIP for approx 18 months. I feel great and got my condition into remission within 5 months of following the AIP way.
So thankful I found your page and to you for your incredible knowledge and insight to the complexities of health and autoimmune.
I am now taking a look into my bathroom products and can’t seem to find a natural body lotion that doesn’t contain nuts or seeds.
How potentially damaging is it to have seeds/nuts in body products for someone with an autoimmune.?
(I do eat almond meal sometimes when baking and don’t appear to have an issue.)
Thank you

foods containing phytic acid have caused my MS. the day that i stopped eating foods high in phytic acid is the day i started to improve. just because there is an absence of studies/data doesn’t mean something is not true.

phytic acid leaks from the gut.
phytic acid crosses the blood brain barrier in rats
phytic acid triggers an immune response that damages my cns

my degrees are in research methods and statistics. this post is not baloney.

john PhD

What about SPROUTED beans and seeds? My understanding is that much of the composition of what you’re eating changes in the process from a seed to a sprout….

Sprouted beans and seeds can be good options, however I would still recommend eliminating them on the autoimmune protocol for at least 30 days before reintroducing them. -Kiersten

I’m sorry, I don’t know what you mean when you say the fiber in nuts can be difficult to digest. Fiber isn’t digested. It’s roughage. That’s why it moves things through your system. Is this a typo? Thanks. :)

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