The WHYs behind the Autoimmune Protocol: Eggs
June 23, 2012 in The WHYs of the AIP
Eggs are one of the most allergenic foods with approximately 2-3% of the population affected. However, people are still surprised when I advertise an egg-free recipe or mention that I can’t eat eggs. It’s not because I’m allergic but because I have an autoimmune disease and eggs are excluded on the Autoimmune Protocol. Given that eggs are such an important staple for the paleo enthusiast (as a breakfast food, as a cheap protein, and as an ingredient in the vast majority of paleo baking recipes), I get asked “Why Eggs?” frequently.
One of the main functions of the white of the egg is to protect the yolk against microbial attack while the embryo grows. It achieves this worthy goal by using proteolytic enzymes (or proteases), enzymes that can cleave proteins into shorter chains of amino acids (typically rendering those proteins inactive/useless in the process). There are many different types of proteolytic enzymes, each highly specialized to cleave a specific type of protein and/or in a specific place. In particular, the proteolytic enzymes in egg whites are very good at cleaving proteins in the cell membranes of certain bacteria (specifically gram-negative bacteria, which I’ll come back to in a couple of paragraphs). The specific protease in egg whites that those of us with autoimmune disease (or severe allergies or severely leaky guts) need to be concerned with is called lysozyme.
I used to use lysozyme in the biology lab to break apart the membranes of bacteria (typically bacteria that I had engineered to grow specific DNA strands for me). Lysozyme is specific for bacterial membranes, works very quickly, is very resistant to heat, is stable in very acidic environments (so it’s still active even after cooking eggs thoroughly and digestion!), and is really a pretty ingenious little enzyme (that’s me geeking out). Humans also produce lysozyme as part of our normal defense mechanisms against bacterial infections. It is present in our saliva, tears and mucus (including the mucus layers in the intestines). So, if we already make our own lysozyme, why is it a problem in egg whites?
Lysozyme has the ability to form strong complexes with other proteins. So, lysozyme from egg white typically passes through our digestive system in large complexes with other egg white proteins. Many of the proteins present in egg whites are protease inhibitors (see this post for more information on how protease inhibitors can contribute to a leaky gut). This means that the lysozyme/egg white protein complexes are resistant to digestion by our digestive enzymes (which are themselves proteases). You might be wondering if lysozyme is still active if it is a protease and it is now bound to egg white protease inhibitors. The answer is yes, it is still active. The egg white protease inhibitors that are most likely to be bound to lysozyme are ovomucin and ovastatin, which are a trypsin inhibitors (trypsin is one of our main digestive enzymes), cystatin, which is a cysteine protease inhibitor, and ovoinhibitor, which is a serine protease inhibitor. None of these inhibitors inhibit the activity of lysozyme. And very importantly, as the lysozyme complex travels (largely intact) through the environment of our gut, lysozyme can also bind bacterial proteins from the bacteria normally present in our digestive tract (like the gram-negative E. coli!).
Lysozyme has an unusual chemical property (it maintains a positive charge) that allows it to cross through the enterocytes by electrostatic attraction to negatively charged proteins imbedded in the enterocyte cell surface (proteoglycans). Research confirms that consumed lysozyme gets into the circulation even in healthy individuals (even in conjunction with food intake, although the amount that enters the circulation is lower). 1,2,3Absorption of pure egg white lysozyme by itself into circulation is likely not problematic because lysozyme is an enzyme that the body naturally produces (unless it is absorbed in very high concentrations and then it can cause kidney damage). The problem is the other proteins that piggyback on lysozyme across the gut enterocyte barrier. It is this “leak” of other egg white proteins that is the reason why egg allergy is so common. Any other proteins present in the digestive tract can potentially bind in the lysozyme complex and get helped across the gut and into the blood stream (or lymph). And because lysozyme binds bacterial wall proteins, these are likely to “leak” across the gut enterocyte layer as well. These foreign proteins are believed to contribute to a molecular mimicry response where the body, in its attempt to form antibodies against these foreign invaders, accidentally creates an antibody that also recognizes a normal protein in the human body.
It’s also important to point out that the ability of lysozyme to cross the gut barrier (carrying potentially immunogenic proteins along with it) is a fairly small effect. In normal, healthy individuals, lysozyme is not likely to cause significant damage to the healthy lining of the gut or cause a substantial immune response (although the effect of lysozyme is why Prof. Loren Cordain recommends limiting eggs to 6 per week). In healthy individuals, pastured or omega-3 eggs can be an excellent, inexpensive source of protein, omega-3 fatty acids, lutein, zeaxanthin, choline, selenium, phosphorus, vitamin A, vitamin D and the B vitamins. However, in the case of autoimmune disease, individuals are more sensitive and tend to have exaggerated immune and inflammatory responses to foreign proteins in the circulation. These individuals are also more likely to form auto-antibodies in response to bacterial proteins that may enter into the circulation with lysozyme.
You might notice here that this discussion was entirely related to egg white proteins. Egg yolks are not likely to cause these issues. However, if you are following the Autoimmune Protocol, I urge caution since egg yolks are a very common food sensitivity in those with leaky guts (note that this is different than being allergic to them). I still recommend avoiding both egg white and yolk when you first adopt the Autoimmune Protocol. But, of all of the foods that are restricted in this protocol, I think egg yolks are the most likely to be tolerated and many people can add them back in.
1 Kondor-Koch C, et al. Exocytotic pathways exist to both the apical and the basolateral cell surface of the polarized epithelial cell MDCK. Cell, 1985. 43(1): 297-306,
2 Hashida S, et al. Concentration of egg white lysozyme in the serum of healthy subjects after oral administration. Clin Exp Pharmacol Physiol. 2002. 29(1-2):79-83.
3 Nishikawa M, et. al. Electrical charge on protein regulates its absorption from the rat small intestine. Am J Physiol Gastrointest Liver Physiol. 2002. 282(4):G711-9.







































Thank you! I love how you put this in such away that I can understand what you are saying.
Wow. Thank you for sharing this. I am wondering what then do I eat for breakfast. I have an 11 year old with an autoimmune disease and fybromyalgia, I have hypoglycemia and my husband has fybromyalgia. So i chose to go paleo for the whole family to hopefully keep other autoimmune diseases and responses from happening if that’s possible. We also do not do dairy. I have also read to not do nuts on the autoimmune protocol. It seems to really limit what we eat. The whole family consists of 6 children hubby and myself.
I eat sausage for breakfast (usually homemade because it’s cheaper) with some fruit and veggies on the side (I especially like sauerkraut and baby spinach on the side). Yes, it is limiting to not be able to eat eggs OR nuts. Other breakfast options are smoothies made with coconut milk (you can try adding egg yolk to the smoothies) or something that looks like lunch or dinner.
I’ve “invented” breakfast salads: salmon, tuna or trout with coleslaw (& my own dressing) & avocado.
this make sense, but adds to my frustration! I have several autoimmune issues (celiac, hypothyroid, psoriatic arthritis, chronic anemia) and just don’t know what to eat anymore. I don’t cook, I am so tired all the time I just don’t have the energy to think about fixing anything. I basically stick to boiled chicken and grass fed beef. I find myself eating less and less, yet never lose weight! Food seems to have become an enemy, except for fruit, which I also should eat too much of. Frustrated!!!
I completely understand your frustration! The only thing I can say is that your energy should increase following the autoimmune protocol. I eat sausage for breakfast (there’s lots of options out there for pastured pork sausage, grass-fed beef/bison/lamb sausage) with veggies and fruit on the side (usually just some sauerkraut or raw spinach since I don’t have alot of time in the mornings). Lunch is typically canned or smoked fish or leftover meat with raw veggies (again it’s fast) and usually a bowl of bone broth. Supper is meat and veggies with fruit for dessert. I get the same thing where I don’t really feel like eating anything in front of me. But I know if I don’t eat, I’ll feel crummy and crave sugar later. It’s easier for me if I have leftovers to grab quickly, so I always try and plan to have something fast. Also, you might not be losing weight because you are eating too little (plus, it’s very difficult for the body to heal if you aren’t eating enough). I’m sorry this is so frustrating for you!
This was great!
I’m always highly interested in why some people thrive on one food that makes another person not thrive … especially when there is no particular allergy
I have always done well with eggs, and often have a couple of hard boiled eggs for lunch… or just one for a super-quick snack.
So here’s my question… do you suggest that I try eliminating eggs from my diet for a month or so, just to see if I feel even better?
Thanks for the good site and fascinating articles….
==>Jimbo Paleo
Ah! Explains why I came back on my blood work with immune complexes to egg white but not yolk. Thanks.
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Great blog, I was hoping this post would answer some of my own questions but it only ended up raising more. I have an autoimmune disease and started to show IBS/Celiac symtpoms a few years ago. All my tests are negative, my allergy tests are negative, I seem to be getting all the nutrients I need, but I always have stomach issues.
But egg yolks (never the whites) make me extremely sick within 10 minutes of eating them. I feel terrible for the next 2-3 days but no one has been able to tell me what’s going on. It didn’t start happening until I was 21 – up to that point I ate scrambled eggs as a regular breakfast my whole life. I can still eat whites and they don’t seem to cause any reaction in me but any trace of a yolk and I’m done for.
I love all your info about the paleo diet, definitely book marked the blog.
Have you tried finding eggs from pastured chickens who are not getting fed wheat or other gluten-containing grains (and probably also not soy or corn)? This can be tricky to find. There is evidence that chickens fed soy have soy proteins in the yolks only of their eggs. And anecdotally, many celiacs report having issues with chickens who are fed gluten-containing grains (it’s possible that gluten is then present in their yolks). This hasn’t been measured as far as I know with gluten, but since it has with soy, that’s my guess as to why you’re having issues with yolks, especially if food allergy and sensitivity tests are showing that you aren’t sensitive/allergic to eggs (just the trace gluten that might be present in them). I hope this helps.
[...] figured out the autoimmune protocol of paleo. I knew from Loren Cordain there would be no dairy, no eggs and no nightshades. Further research revealed I would be avoiding fructose, yeast, alcohol, nuts, [...]
Does anyone know of a food preparation method that would break down lysozyme?
What is your take on duck or goose eggs? My ND recommends eating duck eggs because I tested sensative to eggs on a blood test. Just wondering what your take is on it, because I haven’t seen anyone in the Paleo community recommend replacing chicken eggs with duck eggs for AI protocol. Most of the information I find substantiates her advice and states that most people who don’t tolerate chicken eggs, are able to tolerate duck eggs. Just wondering if you could weigh in on this? Thanks.
Lysozyme is found in all egg whites. Once you heal, you may be able to tolerate some eggs, but until then egg white is best avoided. But, pastured egg yolks do contain some great nutrition. I definitely think it’s worth trying the yolks to see how you do with them.
Very interesting! My son is highly allergic to eggs (and milk) and I am allergic to nuts (tree and peanuts) and many many other things….I came across your blog looking for some recipes (just mixed up the marinade for the asian chicken wings. can’t wait to try them.
I have known I was gluten intolerant for a decade. I was never tested, so I will never know if I would have been diagnosed as celiac. During the time since then I have been very strict about not eating known gluten-containing foods. Along the way I have discovered that I am also intolerant to some of the other foods listed above.
It was hard giving up eggs, because I found it so limiting after having eaten several a day for many years. Recently I discovered that if I throw away all the whites, I am able to eat unlimited yolks daily. I’m sure it wouldn’t work for everyone, but it has worked out well for me.
I can’t even get the cats to eat the whites, and these guys are the worst little thieves imaginable. I think that says something about the food quality of egg whites.
Dear Sarah,
This is the BEST EVER explanation I have ever found about egg allergy!!! THANK YOU! xx
Do you want to know something funny…..When I was 5 years old, and I was given eggs to eat, I always refused to eat the whites, and I loved the yolks!!! I thought the whites were yuck and wouldnt eat them at all, but I loved the rich buttery flavour of the yolks!!! Do you think I was being in touch with my instinct as a 5 year old? Well seeing as I am doing the AIP paleo properly this time, maybe after a couple of months I can re-introduce JUST the egg yolk and see how my body reacts!?….Pity, as I thought that egg whites help people get the lean ripped abs look in weight loss and body building!!
Yes, I totally think reintroducing egg yolks is worth it. And yes, I think you probably did have an instinct about eggs at 5-years old. Maybe when you ate the whites, you got a tummy ache or felt more tired. Food aversions to foods you are actually allergic or sensitive to are actually very common.
Thanks Sarah!
Yes I remember having very weird allergy symptoms as a 5 year old too!! Like spots that looked like water droplets going all the way up and down my arms and legs!!! Wheat upset my bowels, I hated the smell of cow milk too!! I really loved fish!! I was very fussy, I hated cheap sausages because I did not know what bits of meat were in them Lol! I remember I had loads of energy when I had a fry-up like bacon or black pudding, yet as I grew up, all the health info out there taught us that meat was bad for Psoriasis and PsA, and sat fat was bad. I really agree with you, and think that the reason that diets like Pagano Psoriasis diet works in his book is due to removing Deadly Nightshades and Gluten/Dairy. But in the long term, being vegan (gluten free vegan as I was) has other detrimental affects on the body- as I found out for myself!!! I really seriously cannot live without Omega3 Fish oils!!! <3 Maybe one day in my future I will be a Paleo mom too
I have been re-introducing foods slowly. I have successfully added decaf coffee and almonds without any issues. Yesterday I tried eggs. I made sure to eat enough of them throughout the day, a total of 6. I felt fine all day, no apparent issues. Today though I have been extremely bloated and wondering if this is in fact from eating eggs. I am not sure if everyone’s reaction is different or if there are some similarities I should have looked for. Thanks for any help you can give and I cannot wait for your book!
Food sensitivity reactions typically peak between 4 and 28 hours, but can appear any time within several days afterward. Symptoms can be different from person to person and from food to food.
Thanks for the confirmation! Now I know why I always felt the way I did after eating eggs, thought for sure it was always something else! I ate eggs every morning and haven’t for almost 2 months and have been feeling better till the other day.
Hi Sarah, you mention in an earlier response to someone regarding breakfast sausage, “(there’s lots of options out there for pastured pork sausage, grass-fed beef/bison/lamb sausage).” Could you please point me in the direction of some of these options, either to make at home or for purchase in store/online? I’m having a hard time figuring out a palatable breakfast absent eggs (not that I loved them nor ate them frequently before, just now that I’m off my long time go-to breakfast of buckwheat & quinoa hot breakfast I’m at a loss without eggs too..) as the last thing I want when I first get up in the morning is a lunch/dinner like meal.. and so far the only “breakfast sausage” recipes I found online taste just like something you’d make for lunch (spices like oregano, etc). Not being able to have any form of sugar on the Whole30 right now NOR various typical breakfast sausage spices like paprika given the AIP will undoubtedly make it more difficult to find a yummy breakfast substitute, but.. I’m confident they’re out there! Thank you!
I have a question about separating the yolks from the whites. I used the method shown in Youtube videos, of moving the yolk between the two pieces of the shell. Then I rinsed the yolk under tap water, and picked off any visible pieces of white.
Is this enough to remove egg whites, for leaky gut purposes?
p.s. I may be posting a few comment-questions on different articles, because I just discovered your site. Hope that’s alright.
That’s what I do and it works for me. Not sure if that would be good enough if you had an allergy to egg white, but for leaky gut purposes, it should be fine.
… and comments are always welcome!
Hi Sarah,
great information as always, your blog has definately become a staple and much used encyclopedia for me in my way to healing! I wouldn’t know what to do without it
I have a question about supplements when not eating eggs that I just posted on the balancedbites site, but then I thought maybe you know about this too, and since you were so amazingly helpful the last time I posted a question I hope you don’t mind if I copy+paste my post from Diane’s site, and put it here as well. Here it goes:
” I have a rather specific question, and I’m really hoping someone here might be able to help! I have been paleo for about 6 months, and I have your book. I have autoimmune symptoms and a leaky gut, slowly getting better, but there’s still a lot of fixing to do. In Practical Paleo you mention phosphatidylcholine as a supplement that’s useful when you’re avoiding eggs, would that have same effect as a choline supplement? When I looked online for phosphatidylcholine I also noticed that they were all derived from soy, is that ok, or might that be a problem? Would choline bitartrate be better? Which one should I choose when I can’t eat eggs, and my intention is to heal a leaky gut? Thanks in advance for any suggestions on this!”
Hi. I think you have me confused with Diane Sanfilippo who wrote Practical Paleo (her site is balancedbites.com). This isn’t a supplement that I’m very familiar with, so I’m afraid I can’t answer your question.