What Is A Leaky Gut? (And How Can It Cause So Many Health Issues?)

March 15, 2012 in Categories: by

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(Created as a guest post for The Paleo Parents)

One of the fundamental principles of paleolithic nutrition is avoiding foods that damage the lining of the gut.  Essentially, the gut is just a long, wrinkly tube.  Inside this tube, food is digested by enzymes and friendly resident bacteria, breaking down the components of our food to their simplest forms: proteins are broken down into amino acids; carbohydrates are broken down into monosaccharaides; and, fats are broken down into fatty acids.  What can’t be digested by our bodies is excreted as waste.  Amazingly, a single layer of highly specialized cells (called enterocytes) is all that separates the inside of the tube from the outside.  These enterocytes have two very specific jobs:  1) transport the digested nutrients from the “inside-the-gut” side of the cell to the “outside-the-gut” side of the cell; and 2) keep everything else on the inside of the tube.  Immediately outside this tube are two important parts of the digestive system: 1) the resident immune cells of the gut whose job it is to protect against pathogens which might accidentally find their way through the enterocytes; and 2) a network of blood vessels and lymphatic vessels that carry the digested nutrients from our food to the tissues in our body that need them (amino acids and monosaccharaides are transported through the blood while fatty acids are transported through the lymphatic system). 

A “leaky gut” occurs when either the enterocytes are damaged or the proteins that form the tight bond between these cells and hold them together as a solid layer are damaged (or altered).  When this happens, it creates microscopic holes through which some of the contents of the gut can leak out into the blood stream or lymphatic system.  What leaks out isn’t big chunks of food.  Instead, it’s a combination of many different pathogens: incompletely digested proteins, bacteria or bacterial fragments from those friendly bacteria that are supposed to stay inside your gut, or a variety of toxic substances or waste products that would normally be excreted.  When these pathogens leak out, the resident immune cells of the gut recognize them as foreign invaders and mount a response against them (when large quantities of pathogens leak out, other parts of the body, especially the liver, also contribute to the response).  Exactly what leaks out, and how much, determines the precise nature of this immune response. 

 Some pathogenic substances (like bacterial fragments and toxins) cause generalized inflammation by triggering the release of chemicals called inflammatory cytokines (the chemical messengers that circulate in the blood and tell white blood cells to attack).  This type of inflammation has no target so any cell in the body can be an innocent victim.  It is the liver’s job to both control this type of inflammation and to filter out the toxins that may be triggering it.  When the liver is overworked, the toxins build in the body and the inflammation spreads.  This type of inflammation can be a major contributor to health issues ranging from psoriasis and asthma to ADHD and depression.

Other substances (like incompletely digested proteins) cause specific inflammation, which can take the form of an allergy or an auto-immune disease.  An allergy is caused by immune cells creating IgE-type antibodies targeting a part of a protein that is specific to the food it originated from (like an antibody targeting the casein in milk resulting in a milk allergy).  A very similar type of immune response is caused by immune cells creating IgA-, IgM- or IgG-type antibodies targeting a part of a protein that is specific to the food it originated from.  This type of immune response is technically considered a food sensitivity (and not an allergy), and can cause both allergy-type symptoms and symptoms that you might not normally attribute to an allergy, such as: pain, fatigue, and eczema.  It is also the formation of these types of antibodies that can cause auto-immune diseases.  Antibodies target only a short sequence of amino acids, and not all of the amino acids that form an individual protein.  In the case of food allergies and sensitivities, this short sequence of amino acids is still specific to the food it originated from.  But, sometimes the antibodies that form in response to “leaked-out” proteins target a sequence of amino acids that isn’t unique to that protein, but instead is a sequence of amino acids also found in many other normal proteins in the human body.  When this happens, the body attacks itself thinking its own cells are foreign invaders.  For example, an antibody could form against a sequence of amino acids that is found in the insulin-secreting beta cells of the pancreas.  When the body attacks those cells, it causes Type I Diabetes.  An enormous range of autoimmune diseases can be caused in this way, from lupus to celiac disease to Graves’ disease (many of which include genetic susceptibility as confounding factor). 

It is important to know that, for some individuals, a leaky gut can develop slowly over years or decades.  Stress, sleep-deprivation and/or some infections can make matters worse very quickly (and unpredictably).  Once you have a leaky gut, it is only a matter of time before related health conditions begin to crop up.  Depending on the extent of the damage to the gut lining, the exact substances that leak out, and your specific genetics, the inflammation and immune reactions caused by having a leaky gut can add up to any of a huge variety of different health conditions, many of which can be life-threatening.  This is why the gut-friendly, anti-inflammatory paleo diet is known to address so many different health issues:  if your gut is healthy, then so are you.


If only such important information were available ‘back-in-the-day’ I would not be suffering so. I’ve dealt with lupus all my life and NEVER have I encountered such wonderful information! Having just read an article from the Lupus Association, there was a mention of ‘nightshades’ and I had no idea what they were talking about. That article lead me to you. Praise the Lord I found you!

Hi! I have a question about leaky gut. I have been trying to solve a problem for the past 4 years and have tried so many different things with trial and error and I haven’t been able to pin point exactly what is wrong. My blood test shows elevated liver enzymes and high bilirubin and I also experienced intussusception of the small intestine and flare ups on my scalp. My question is: Do you think this could be caused by leaky gut or some kind of food allergy? I typically experience discomfort on my upper left side after some meals and I have random flare ups of seborrheic dermatitis on my scalp. Fatigue and mood swings can also follow.. I’ve tried elimination diets and I haven’t quite been able to pin point the problem yet. Do you have advice on what to try next or thoughts about the root of the problem? Thank you!

Hi Vince,

I had the same. Horrible itchy scalp and only one dandruft shampoo which would calm it down.
Since I eliminated dairy, grains and legumes from my diet I have nearly no itchy and flaky scales. I can wash my hair with normal shampoo too. Every now and then I do eat some beans or a product with milk or grains in it and the first things I notice is that my scalp flairs up. Hope this is helpfull.

I just saw your reply and would like to hear more about how things with your scalp and gut have been. I have been trying no gluten, dairy, sugar and alcohol and have become very suspecting of dairy but never heard of legumes are being a problem. So grains, legumes and dairy are the main culprits for Leaky Gut and having an itchy scalp. Did you experience hair loss from the itchy scalp?

Thank you for this article! My doctor just diagnosed me with chronic inflammatory response syndrome. It’s inflammation all over your body and I assume is related to leaky gut because I was also diagnosed with biotoxin illness from toxic mold. I have skin rashes, constant nausea, continuous headache and chronic swollen lymph nodes. Things would have been so much worse if I wasn’t already following a paleo diet. Now I’ve got to be on a low amalose diet but I don’t know what that is. I heard its similar to low histamine diet. Any suggestions?

Hi there, I have just done 45 days of the AIP diet and am now introducing food. I am doing this to prevent autoimmune disease which I have in my family history but also to help with endometriosis. I used to get eczema as a child and have noticed I get itchy after re-introducing certain foods e.g. dairy and chocolate. Just wondered if I can do the IgE blood tests for all foods and spices and will this just tell me what foods I should avoid to help with gut healing? Is the Ige test the same as the RAST testing? Is this useful for us trying to heal leaky gut and prevent autoimmune disease?

Love the Blog so much. It’s been an absolute fantastic help in figuring out and more importantly explaining my recent diagnosis (Hashimoto’s) to friends and family. I’m fascinated by the science you lay out here. I’m wondering, if the negative autoimmune response is brought on by a sort of miss identification by the immune cells would it be possible to pinpoint what protein sequence is causing the flare up and it’s ‘look a like’ that is already in the body. I think what I’m asking is once it’s a case of mistaken identity will the immune system attack any short system amino acids in my body even if I steer clear of ingesting the guys that make it act crazy? I’ve not studied science at any length so correct me if i’m wrong, but as I understand it it’s sort of like racial profiling. The immune system, antibodies (police) arrests a bad hunk of cheese (ethnic minority) now the antibodies (cops) thinks that all the amino acids that look like the guys they caught are the same. So all the ethnic minorities (amino acids) in the neighborhood are getting beat up by the cops (antibodies) without due process (enterocytes). Simplification I know, but if one were able to identify what the amino acids that came with the cheese are could we know to avoid those so that the antibodies don’t also attack the good guys that are already apart of the system? Oooor am I way off base. Again science was never my strong suit.

I understand that for ppl who have autoimmune diseases that even cheating with a spoonful of some thing non AIP will flair the immune system and it won’t calm down for months. Does this happen only to autoimmune diseased people? No one seems to ask this question but is it necessary to follow AIP if you do not have an autoimmune disease but only have the leaky gut? Read the book, but it seems to be specific to autoimmune issues… Thanks

Could I please get the source for this information please? I would like to learn more on this topic by reading the relevant journal articles that this information comes from.

There is an extensive reference list in The Paleo Approach and it goes into leaky gut in a lot of detail. -Kiersten

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