The WHYs behind the Autoimmune Protocol: Alcohol

November 8, 2012 in Categories: by

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Alcohol is restricted in the paleo diet autoimmune protocol; and for those of us with autoimmune disease, it can feel like there are no pleasures left!  My inner monologue goes something like this “Seriously, first I give up grains, legumes, dairy, modern vegetable oils and refined sugar.  THEN, I give up eggs, nightshades, nuts, seeds, coffee and chocolate.  And NOW you want me to give up my wine?!  I thought red wine was supposed to be good for me! Waaaaaaah

Moderate consumption of alcohol (not just red wine) seems to provide diverse health benefits; including reducing the risk of cardiovascular disease 1, reducing the risk of developing type II diabetes 2, preventing Alzheimer’s disease 3, and it may even reduce the risk of some cancers 4. (Don’t get too excited about the cancer prevention piece… moderate alcohol consumption also increases the risk of other cancers.)  While alcohol is not technically paleo, there is certainly evidence that prehistoric man would have imbibed fermented fruit and probably got pretty darned stinkin’ drunk from time to time.  Almost every version of the paleo diet condones low to moderate consumption of alcohol (usually restricted to gluten-free alcohols, so mainly wine and spirits), including Prof. Loren Cordain and Robb Wolf.   It is a Neolithic pleasure that most people following a paleo diet still enjoy.

So, with all the research supporting that moderate consumption of alcohol (especially wine) is healthy, why is it then a problem for those with autoimmune disease?  Once again, it boils down to the fact that those with autoimmune disease have more sensitive systems and face more challenges to healing a leaky gut than others.

Alcohol consumption directly causes an increase in intestinal permeability (i.e., a leaky gut) 5.  Alcohol unravels the tight junctions and adherens junctions that glue the cells that line the gut (called gut epithelial cells or enterocytes) together to form the  barrier between the inside of the gut where undigested food and bacteria live and the inside of our body.  Effectively, alcohol creates little holes between the gut epithelial cells.  It does this through several mechanisms 5Importantly, the “holes” that alcohol makes in the gut epithelial barrier are known to be big enough to allow some very large molecules into the body, most notably endotoxin.  Endotoxin is a toxic protein derived from the cell walls of gram-negative bacteria, such as E. Coli, which live in our guts (usually in the large intestine, but often in the small intestine in those people with autoimmune disease).  As these bacteria die (as part of their normal life cycle), endotoxin is released.  If it gets into the blood stream, it stimulates systemic inflammation, stimulates the immune system, and damages the liver 5.

Normally the majority of bacteria that grow in our guts are gram-positive bacteria (although some gram-negative bacteria is normal).  What does gram-negative and gram-positive mean?  This refers to a staining technique that differentiates between these two major classes of bacteria.  Basically, gram-negative bacteria have more complex cell membranes/walls and these tend to be pathogenic (i.e., they cause disease).  E. coli is an example of a gram-negative bacteria.  Lactobacillus (the probiotic found in supplements, yogurt and fermented vegetables) is an example of a gram-positive bacteria.  So, here’s the kicker:  alcohol consumption feeds gram-negative bacteria such as E. Coli to create bacterial overgrowths of these more toxic bacteria and therefore excess endotoxin production in the gut.  Excessive alcohol consumption is also correlated with gram-negative bacteria growing very high up the digestive tract, in the duodenum and sometimes even the stomach 5,6.

So, alcohol increases the production of endotoxin within the gut and increases intestinal permeability to endotoxin.  Another toxin that is produced by both gram-negative and gram-positive bacteria is called peptidoglycan (another component of the cell wall that is released into the gut when the bacteria die).  There is evidence that alcohol increases the permeability to peptidoglycan and that this toxin is very effective at stimulating the immune system and causing inflammation 5.

And that’s not all.  Even fairly small amounts of alcohol can damage the lining of the gut; specifically, alcohol leads to “mucosal damage in the upper small intestine with a loss of epithelium at the tips of the intestinal villi, hemorrhagic erosions and even hemorrhage in the lamina propria” 5.  If that sounded bad, that’s because it is.  It’s similar to the damage caused by gluten in celiac patients.

Most of the current understanding of the link between alcohol consumption and increased intestinal permeability (a.k.a. leaky gut) comes from studies of chronic alcohol consumption.  But, there are studies to show that this damage occurs even from a single drink.  Occasional drinkers basically don’t damage their intestines as much because they don’t consume as much alcohol at one time and they have more time for the guts to heal in between drinks.  This might lead to some adaptive mechanisms, which might be part of how low-to-moderate alcohol consumption can actually provide a health benefit.

So, what does this mean for those with autoimmune disease?  If you have autoimmune disease, you have a collection of genes that makes you more susceptible to developing a leaky gut and to having an exaggerated immune reaction to substances that leak out.  This means that anything that increases intestinal permeability should be avoided.

There’s some good news.  If you are being very strict with the autoimmune protocol, you are likely to tolerate an occasional drink (make sure to stay away from any grain-based alcohols though, especially beer and ale which contain gluten).  Chris Kresser puts the limit on one 5oz glass of wine twice per week (or equivalent amount of hard alcohol that is not derived from grains such as rum, tequila, sherry, cognac and brandy).  However, I advise avoiding all alcohol until you are starting to see some success on the autoimmune protocol. 

There’s some other good news.  It’s actually the alcohol that is the problem here, which means that cooking with wine or hard liquor (where the alcohol is burned off in the cooking process) is totally okay.  Well, with one more caveat:  some people are can be sensitive to the yeast content of wine (the yeast used in wine fermentation is a potential gluten cross-reactor) or can be sensitive to the the sulfites found in wine.

In summary, alcohol is not good for anyone dealing with leaky gut issues.  However, an occasional drink once your body is healing is probably okay.  Cooking with alcohol is also probably okay for most people, even if you don’t tolerate an actual drink.  But once again, I do urge caution as you experiment to find where your individual line is.


2 Mekary RA et al “Joint association of glycemic load and alcohol intake with type 2 diabetes incidence in women” Am J Clin Nutr December 2011 ajcn.023754



5 Purohit V et al “Alcohol, Intestinal Bacterial Growth, Intestinal Permeability to Endotoxin, and Medical Consequences” Alcohol. 2008 August; 42(5): 349–361.

6 Sekirov I et al “Gut Microbiota in Health and Disease” Physiol Rev, 2010 July; 90( 3): 859-904


This explanation is very interesting. Before going on the AIP, if I evern had more than 1-2 drinks, I would wake up the next day with my whole body feeling tender to the touch. Now I know that was probably due to systemic inflammation from the alcohol. Even one glass of wine would sometimes put my stomach over the edge for days. It truly is something to be avoided to heal the gut.

Thank you for your excellent piece. I am 85 percent managing leaky gut syndrome — always managed, never cured — and had social reasons to limit my alcohol. Recently I tried a great single malt and a couple of days ago a nice cognac. Both times I had a gut clearing experience which is now totally explained, my gut sensing the presence of the alcohol and responding by moving things along. It was the gut protecting itself. I also have vagal AFIB and an upset gut tends to set off an episode, so maintaining a gut in balance is important. Your explanation was just what I needed to put all of the pieces together. I suspect that a tiny bit of the cognac, or liqueurs that are mainly for inhaling could allow for some appreciation without impact on the gut.

Thank you for this. I found Paleo due to a number of food intolerances, including yeast (baker’s and brewer’s) and concord grapes to name a couple. So I’ve been staying away from alcohol, which was only used for cooking anyway. I know I still can’t use it, but it helps me so much to know why. All of your explanations have been so helpful for me in that. I am one of those people who needs to know they whys in all of this too. Your explanations are easy for the average person to understand. Thank you.

Bummer! I so didn’t want to hear this. But, to be honest, I think I’ve been in denial for awhile-on numerous occasions I’ve woken up the day after having had a glass of wine with dinner and noticed that my joints were a little achy. The ache isn’t that bad, and I love a glass of wine every now and then, but I’m more concerned about my gut health! Without a healthy gut how can I have healthy anything else?!

I have never been able to drink alcohol. Even small amounts of it whether it was wine, beer or hard liquor would trigger a migraine in me (though cooking with alcohol never seemed to bother me). It was like going straight to the hangover without the fun of getting drunk. This is probably why. Thanks for posting.

Great post. Yes…I’ve been in denial for a long time and will just have to swallow the truth – so to speak. I very much relate to the opening para in your post about the inner conversation. I have this almost daily! Somehow, white spirits do not affect me as much as wine. Still, I feel that neither is good for my health and well-being. Thanks.

Wow! Explains why even that occasional glass of red makes me wake up with a headache and allover achiness. Thanks for the wake up call.

This is such a great explanation of all of this. Over the past several years, I’ve become more and more intolerant to alcohol. Gluten drinks went first, and then, my favorite, wine, which always exasperated sinus problems. And then went my next favorite, whiskey, and everything else really. Drinking alcohol gives me severe sinus pain and causes mucous production, makes me feel severely “hung over” the next day, even the smallest amount, and in the days following consumption, I usually get a full blown sinus infection and joint pains. I’ve begun to focus on an Autoimmune Protocol but I know I’m a long ways away from tolerating alcohol again considering my intense reactions. Thanks for such a great post.

Sarah, quick question. Since you allow cooking with alcohol, knowing that some of the alcohol remains after cooking (up to 40% depending on heat and cooking time), does that mean uncooked flavor extracts with tiny amounts of alcohol would be fine as well? i.e. a teaspoon of vanilla extract, peppermint extract, etc.

I love your information, but…(always a but)… Did you know that stress is another one that causes gut leakage?…and is very stressful for a person like me that suffers of IBS to read way to often that I can’t eat wheat, nuts, nightshade veggies, coffee now even a glass of wine?…:/ … I have being free of gluten for 4 mos. and I have being able to drink a little coffee and a glass of wine occasionally I have being talking to a Quantum Albhabiotic/ Par Biomagnetic therapist and I’am hoping I can heal my gut some day so I can enjoy some of the good things in life …I probably will stay away from wheat forever but a coffee in the morning and a glass of wine for dinner, shouldn’t be a problem…I agree , sometimes these choices , I can feel them , they hurt, and the reason may be that what we eat with our minds first makes a difference in how our gut reacts, so free yourself from bad thinking and I think pretty much we can enjoy of some of the little pleasures in life. :)… thank you for all the good work!

I don’t drink at all, however have a question! What about the amount of alcohol in daily tinctures from a naturopath? If taking a half teaspoon twice a day but it’s made with a concentrated alcohol, is that going to have a negative effect?

Sarah recommends avoiding all alcohol during the elimination phase of the AIP. Whether or not you add it back in depends on how well you tolerate alcohol and also whatever the alcohol is made from. Even a few drops of any kind of alcohol makes me feel awful, but I know others that tolerate it okay. – Christina, Sarah’s assistant

Does anyone out there actually see a benefit or lessening of symptoms with alcohol, or with a hangover? I do. It’s the only thing all these years that has actually helped me. In doing the autoimmune protocol, it is by far the hardest thing for me to give up, as I find myself lying in bed much of the time, without the one ‘medicine’ that helps me along. Some doctors have suspected it causes a beneficial neurotransmitter change, or the calming/deadening of the part of my system that is out of whack. I know of one other woman with chronic fatigue like symptoms that has had a similar experience. It’s nice to be able to have a whisky, it’s also a dangerous and unhealthy helper. But the phenomena must be able to provide a clue. I have MS type symptoms of extreme periodic weakness, undiagnosed, and have had them over 20 years. Many days I use a cane or can’t walk well enough to leave the house….hungover though, I can always walk. Any ideas? Or resources? Thank you. And Sarah, thank you for all of your amazing work, I just bought your book, and it’s incredibly well put together. You’re helping a lot of people…. tara

Hi Tara,
I have had similar experience to you regarding alcohol intake: In addition to strict diet and lifestyle (AIP), The only way I can be assured to be functional in the morning is to drink the day before. For me, a moderate daily alcohol intake — at least 4 oz of distilled, non-grain hard drink such as brandy/cognac, rum or tequila, diluted in water- combined with a strict AIP diet, balanced exercise, rest, and breathing-awareness, has been very practical.
Though I would prefer to stop drinking, I find myself with anxiety, difficulty moving, persistent insomnia, and mental/emotional lethargy, when I eliminate alcohol for more than a day or two.
Several attempts to give-up drinking have resulted in increased anxiety and insomnia, until I can no longer tolerate/function and I give-up my sobriety and start to drink again. Weaning (systematically reducing alcohol consumption over several weeks) seems an appropriate experiment which I am soon to undertake. A nutritional consultant, using hair mineral analysis, recommended that I would be able to stop drinking as I overcame mineral imbalances, but I could not afford the supplements.

Thank you to Sarah for excellent, informative, researched information. It has been very helpful on this journey.



Thank you so much for writing Zara. Nice to know there’s someone else out there following the strange but somehow helpful healing routine that I am. I hope it continues to work for you. I keep assuming that as my body heals, and my chemistry stabilizes in other ways, that the symptoms abated by alcohol will become less and less, and require less and less. I hope that’s true for both of us.

Last week I cooked a roast in red wine in crock pot….oops, total allergy nausea & headache. The only alcohol I can tolerate is the frozen margarita..

I have Hashimoto and have been following a very strict Paleo diet for more than a year trying to heal my gut. I basically live on more or less 20 ingredients which I alternate and change the way they’re cooked. I never completely gave up the alcohol, occasionally having small amounts of tequila and recently tried one glass of home made wine (no chemicals, yeast or sulfites). After not having wine for one year, I was pleasantly surprised to see I had no bad reactions (no pain, hair loss, tiredness, bloating, hang over, diarrhea etc or other type of discomfort). However, when I have alcohol, I make sure I always drink plenty of water, take probiotics, glutamate and Repairvite (from Apex). I am not saying that alcohol doesn’t cause any damage to my gut while I take it, but I do not have any bad side effects if its in moderation and if I prepare my gut for it before and after by increasing the amount of healing goods I normally take. I don’t drink any other alcohol, coffee, black tea etc… so this keeps me sane while I stick to the diet.

I can attest to this being true having done AIP (minus vanilla bean powder) for 35 days in November and was symptom free for 3 weeks. That is the longest I’ve gone yet and as soon as I threw some alcohol in I was ***ucked.

I also noticed putting some coffee back in also made me whacked out. Right on Sara – I’m expereincing what you share here first hand.

i am just beginning with my auto immune protocol due to my sons reactions to so many foods. i’m still nursing him so anything i eat makes it’s way to him. does that go for the alcohol too? i know that i give it a good two hours before nursing him after a glass of wine. do you have any references or resources for this sort of thing?

Ahh. I’m struggling with the alcohol thing. I was doing good and even shedding pounds then I found a bottle of vodka in my kitchen last night. I served it to my guest with orange juice and didn’t think about it. Then while we were moving stuff I found myself doing shots of it. Low and behold I had diarreha today and I’m inflamed 4lbs. I now realize once again how important it is for me to cut this habit all together. So here I go starting week 1 again.


Thank you for this information, your website, podcasts and other resources are tremendously helpful.

I have a question about best options when one would like the occasional drink. I have hashimotos and celiac disease and have been following the AIP protocol through my functional medicine and neuro functional medicine practitioner’s for 2 months now and have noticed some improvement. I was paleo for 2 years prior. I was never a big drinker but would have the occasional vodka soda (potato) or glass of red wine. I had food allergy testing done through Cyrex. My intolerance alcohol were to red wine and potato. I am not planning to consume any alcohol for at least another 6 months but when I do I wish to make sure I am making the best possible choice (1-2 on special occasion). What would the best choices be of the following; gin (most seem to be grain based although I heard on one of your podcasts this is consumed in the Paleo community), vodka, red wine, white wine and champagne or prosecco? Could you please kindly explain why?

Thanks so much for the work you do.

Kind Regards,
Michelle Maillet

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