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What Causes Gluten Intolerance?

Learn how PUFA-rich seed oils and sugar promote inflammation that underlies gluten intolerance

A pizza crust, a loaf of French bread and a plate of spaghetti walk into a bar. The bartender says, “What can I get you fellas?” and the pizza crust says, “Some Pepto Bismal. We all have horrible stomach aches.”

Not very funny, is it? That’s because gluten intolerance is no joke.

Every year, I see more patients with rashes, or intestinal and joint pain who find that cutting out wheat has helped. But realize that when you have any allergy at all, be it to wheat or cats or carpet glue, the root of the problem lies not in the thing you’re allergic to, but in your immune system. So while it’s important to avoid whatever you are allergic to, it’s also important to realize that your not really treating the underlying issue by avoiding it. You are reducing symptoms, of course. But to get to the root of the issue you have to fix your immune system function. That’s what eating better is all about.

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Left to right: lichen planus, intestinal inflammation, dermatitis herpetiformis. Each results when you develop a rogue antibody that attacks your own tissue. An anti-inflammatory (Traditional/4-Pillar/Deep Nutrition) diet can lead to resolution of symptoms.

Meanwhile, we have popular theories speculating as to why wheat gluten is particularly dangerous sprouting up everywhere. So let me try to put some of the most common to rest.

Why is Wheat Gluten Upsetting Your System?

Pop Theory: Modern high-yield wheat is so different from wheat grown 10,000 years ago that it’s been rendered unsafe to eat.

My take: All crops have been bred to be high yield; wheat is no exception.

Pop Theory:  Man evolved as a hunter-gatherer, and shouldn’t eat wheat because it is an agricultural product.

My take: All vegetables (and fruit) in our stores are agricultural products, and I don’t think it makes sense to avoid eating vegetables.

Pop Theory:  Wheat is a grass, something human beings are not adapted to eat.

My take: Rice is a grass, and few people are allergic to it.

Pop Theory: Gluten is an anti-nutrient and in the past we’d sprout seeds to neutralize the anti-nutrient.

My take: An anti-nutrient is a compound that binds nutrients so that they are not available to our bodies and thus pass right through us, unabsorbed. Gluten does not fit into this category and therefore is not an antinutrient. I agree with their stance on sprouting, however. While not neccesary for the body to process gluten, sprouting does facilitate the processing of other components in wheat and I highly recommend sprouted grain products whenever they are an option to you.

Inflammation is the Underlying Cause of Gluten Intolerance and Celiac Disease

Now, I acknowledge that it’s become very fashionable for doctors and alternative practitioners to talk “underlying causes,” but what’s wrong with the above theories is that they fail to consider that the underlying cause of gluten intolerance and Celiac disease is not some inherent problem with gluten (the protein in wheat that makes bread doughy). The underlying problem is that people who have gluten intolerance and Celiac disease have white blood cells that are running amok.

White blood cells work for your body’s immune system. Their job is to patrol your tissues, literally by crawling through them, in search of invading microbes. But when you have gluten intolerance, there are some white blood cells working for your body’s immune system that can’t quite do their job.

It’s not that their lazy. It’s worse: they’ve become disruptive. Think of these disruptive white blood cells as a pack of fraternity brothers after a night of drinking Red Bulls and Vodka—hopped up, aggressive and easily confused. It’s not their fault. It’s your fault. Because somehow you’ve created a situation where your white blood cells just can’t operate normally. This sort of situation is usually a result of eating foods that promote inflammation. (See Video. BTW at some points you may need to pause to read the captions…it runs a little too fast at time, sorry!)

How Inflammation from Processed Foods Promotes Gluten Intolerance and Celiac: Video

Normally functioning white blood cells follow a clear cut protocol that goes a little like this. If, say, an invading bacteria enters the body, a special kind of white blood cell attacks it without mercy. It then keeps a kind of record of the invader, called an antibody, for later reference so that other white blood cells besides that special kind can recognize it, too. It’s like giving a photo to the bouncer guarding the front door and saying, “If this dude ever shows up again, pin this photo to his chest to identify him so that all the brothers know to escort him off the property.”

The immune system even has special T-cells that chaperone this activity, playing the role of the levelheaded president of the fraternity. If the white blood cells start attacking the wrong thing, these special T-cells call off the attack, saying, “Hey, settle down! It’s cool.”

But what if the fraternity president could no longer keep the overzealous pledges in check?

On a typical American diet rife with sugar, carbohydrates (which turn to sugar once digested) and toxic vegetable oils, our bodies are in a constant state of inflammation. And inflammation impairs the immune system’s ability to self-regulate. It’s as if the president of the fraternity—the responsible one—were passed out next to the keg while the young men in his charge run amuck.

The Inflammation-Indigestion Connection

Here’s how this can lead to gluten intolerance. Processed gluten in, say, a snack chip, is—much like a polyunsaturated molecule in processed Canola oil—distorted, an unnatural shape. In the stomach, this strange shape elicits the attention of the immune system (something that appears foreign enough to get the immune system’s attention is called an adjuvant). The immune system attacks this adjuvant and then creates antibodies in case it ever shows up again.

The particular problem with distorted gluten is that it bears a likeness to certain molecules in the tissues of your body, so mush so that these tissues wind up getting tagged with antibodies. When the white blood cells see those tags, they do what they’re supposed to: attack.

When this attack happens chronically, it can start to hurt, especially in the gut and joints. This is celiac disease. And the attack won’t cease until the president of the fraternity sobers up, which is to say, until the chronic inflammation finally subsides.

That’s why I consider gluten intolerance and celiac as a symptom of underlying inflammation. This means avoiding gluten is only the first step. To address the underlying cause, we need to eliminate pro-inflammatory foods.

Speaking of which, a sourdough loaf says to her psychiatrist, “I think I’m gluten intolerant.” The psychiatrist says, “Aha! A classic case of self-loafing.”

Okay, that one is a little funny.

Learn more

Read about why your immune system malfunctions and how celiac causes joint pains on this post.

Find some outside the box breakfast options on this page.

Food Rules: A Doctor’s Guide to Healthy Eating summarizes the principles of anti-inflammatory shopping, cooking, and mindful eating. I recently heard from a woman who read the whole thing in an afternoon at the beach and went home, rearranged her kitchen, four months later she lost 40 pounds and was off all her medications.

This piece is also posted in the Napa Valley Register.

With over two decades of clinical experience and expertise in genetic and biochemical research, Dr. Cate can help you to reverse metabolic disease and reshape your body.

Please note: Please do not share personal medical information in a comment on our posts. It will be deleted due to HIPAA regulations.

This Post Has 40 Comments

  1. Just to be sure, sourdough bread/crackers are safe if going gluten free?

    Thanks for your good work. Been on 4 Pillars diet all month and feeling sooooo much relief. Committed for life, and fine-tuning to relieve persisting symptoms.


  2. I wont touch soy either!!Gives me a horrible itchy rash, but it is a different rash to the gluten which is a more typical dermatitis herpetiformis.

  3. If celiac is really inflammation coupled with an over-active immune response, can celiac then be “cured”?
    I’ve been gluten-free for 9 years. Specifically, I have non-celiac gluten sensitivity. If my health improves, could I have moderate levels of properly prepared gluten again? How can I tell, without just trying it and hoping it doesn’t give me food poisoning (which is how my body reacts to gluten)?

    1. I do believe celiac can go into remission, like rheumatoid arthritis, and that some people may even be able to eat gluten in the context of whole foods once again. This would not be something I would advise without working closely with a practitioner who understands all these issues and that you trust.

  4. I’m a Biologist and I find the arguments put forward by Robb Wolf and other ‘paleo’ folk about the seed part of plants being difficult to digest as a protective mechanism by the plant to avoid their offspring being destroyed. I also agree with their concerns about dairy.

    But what is more compelling is being so well on a NO GRAINS NO DAIRY NO LEGUMES diet. After years of being horribly sick (aches, lethargy, flatulence, rashes, thrush) and having doctors give me pharmaceuticals that didn’t help but had side effects and resulted in terrible anxiety related to going to the doctor. I now have dramatically better health at 40 than I did at 25!!!!

    I think you are playing down the impact and prevalence of Coeliac disease and gluten intolerance and the connection it has with dozens of other illnesses including diabetes, autism, depression etc etc etc.

    1. I’ve never seen this mentioned before but I wonder if all the studies of wheat consider the possible confounder of soybean oil which is almost always accompanied by wheat and other grain products.

  5. Hi Dr. Cate,

    I have PCOS and I am about 30 pounds overweight (after having a baby a year ago). I have a fasting glucose that hovers between 104 and 111. I have deep nutrition and I am currently making dietary changes. I have read in other places that there may be a connection between PCOS and gluten intolerance/sensitivity. What do you think? Also, I believe the reason I was able to get pregnant was by taking a supplement, D-chiro-Inositol, along with a moderate low carb diet and exercise. But it wasn’t until I started the supplement that I became regular again. Each time I mention the supplement to doctors I get the standard response, they are unregulated, don’t’ know what you are getting. I feel the company is reputable and they do some quality control. Now, I see my glucose and weight getting out of control, but because I am still breastfeeding I am hesitant to start taking it again. I know you are not generally a fan of supplements, but can you hypothesize a connection between PCOS, low inositol and gluten? One final question. If you suggest 100 g of carbs per day to start with, how many grams of proteins and fat per day? I want to start slow, I don’t want to lose weight too fast and cause too many toxins to be released which may contaminate my breastmilk. So, I am thinking 100 grams of carbs per day and cut out wheat that isn’t sprouted.

    1. The only plausible connection between PCOS and gluten intolerance is correlative, not causative. In other words, while people can be affected by gluten intolerance and PCOs, I can’t see how gluten could cause PCOS. PCOS is a metabolic disease that stems from hormone resistance and is closely associated with insulin resistance and the advice I give in DN (100gm carbs or less) should still apply!

      1. But insulin resistance is connected to Gluten sensitivity!
        ?Diabetics are 50x more likely to have celiac disease
        ?Gluten directly damages islet cells, the pretty cells of the pancreas that make insulin
        ?Patients with celiac disease have high levels of diabetes- and thyroid-related autoantibodies that resolve when the patients are placed on a gluten-free diet (Ventura, J of Pediatrics, Aug 2000)
        ?Babies exposed early to gluten-containing cereals have a greater risk of developing diabetes later in life

  6. Einkorn and spelt are not the same; einkorn is somewhat older and has a different gluten. However, some people can also tolerate spelt just fine.

  7. Very interesting, as usual. Incidentally is sourdough rye a safer/better choice than wheat and is spelt the same as einkorn (from a home-baker and concerned mother!)

    1. I have heard that the bacteria involved in the production of sourdough break down gluten. Unfortunately, I do not have a source to back up this claim. Has anyone heard this before?

  8. Thank you, Dr. Cate, for explaining gluten intolerance in such clear terms and for the pictures of the rash.

    After visiting the dermatologist for such a rash, I was tested for celiac diseaes, which came back negative. I now understand that underlying inflammation could be the cause of multiple new sensitivities I have developed.

    I have just finished reading Deep Nutrition–my children have Ehlers-Danlos syndrome, which affects their collagen. I have long felt that although they may have a genetic predisposition to such a problem that something environmental has triggered this issue. Thank you for giving me the scientific knowledge to back up my belief.

    We have just cleared our kitchen of vegetable oil and are weaning the sugar (why is that one so difficult?)! Looking forward to seeing how these dietary changes affect their health!

    1. Congratulations on your successful changes so far. The best thing for weaning kids off sugar (aside from patience and at time) is helping them love new foods. The best way to build healthy food habits is giving them new foods when they’re really hungry, like after playing outside all afternoon. Just a taste! They dont have to finish. Gradually, they’ll begin to want it.

  9. Has the consistent consumption of breakfast cereals in the past two generations (boomers and gen x, y) been linked to gluten intolerance? Were these breakfast cereals boosted with manufactured gluten to reduce the production cost to the manufacturer, and increase the weight in the box? Where did this gluten come from?

    Is this one of the reasons that more people have an intolerance, such as the peanut allergy caused by introducing it into many lotions and foods in the 1970’s?

    Has anyone studied this? I am sure that General Foods would not agree, but it would be quite interesting to be able to know the root cause of the intolerance, other than DNA. Some DNA types just ate more cereal than others, because they were given that processed food by their middle class working mothers?

    1. Dr. Davis has studied this in some depth, and discusses that in his book. Most of the evidence is anecdotal, and is likely to remain so, since the folks with pockets deep enough to fund the type of research that would prove that link are profoundly interested in *not* finding such a link.

      Which is one of the reasons I consider my n=1 experiments to have more validity than most of what passes for “science” in the field of nutrition. My motivation is different. I’m interested in discovering what works, not in selling an expensive medication.

      While Dr. Davis does come off as monomaniacal about wheat, I think he is essentially correct in his assessment of effects of the changes done to wheat in the 1970’s. Despite the lack of credible research, it’s pretty clear that wheat elimination has a positive health impact in the vast majority of people, even those who are not celiac. I’m not celiac, and the “medical” establishment did not detect any gluten sensitivities in me — but I’m old enough to clearly remember a doctor who told me that second-hand smoke couldn’t possibly be a problem, just before putting out his cigarette.

  10. Great info, thank you very much! I can’t wait to read the links you’ve provided in the comments, as well. I feel so much better without grains, but I sure would like to be able to enjoy some homemade sourdough from time to time, perhaps made from sprouted einkorn? (With Kerrygold slathered thick enough to see teeth marks, a la Sally Fallon Morrell! 😉 )

    Just a quick edit note:
    “The Inflammation-Indigestion Connection
    Here’s how this can lead to glucose intolerance.”
    Pretty sure you meant gluten, not glucose? Or did I misunderstand?

  11. Ok, but what is “unprocessed” gluten? In other words, how can you get gluten from a grain without processing it…?

    1. You cant! The removal of gluten is one potentially harmful processing step but not as harmful as the use of gluten in extruded foods (like cereals) or combining that gluten with vegetable oils and then baking it (snack foods/crackers ie. those yellow goldfish).

    1. Yes! Good eye. More on why here, and to highlight the difference between native gluten and processed one is represented by a gun that looks like a toy and the other like a threatening weapon.

  12. I couldn’t agree more regarding your prescription to eliminate processed foods and reduce inflammation. However, your comment regarding the WAP Foundation’s stance that humans only very recently began consuming cereal grains without first soaking, sprouting, fermenting or sour-leavening them, being a “pop fad” I find to be ludicrous, and ultimately undermining of your otherwise stellar message. Surely doctor, you must know that these traditional methods of grain preparation pre-digest gluten.

    1. I don’t believe the advice to sprout is faddish and actually edited the article from what it was originally (as still posted on the Register site b/c I can’t change that) so that my point is clear. My point is gluten is not an anti-nutrient. Since gluten is not an anti-nutrient, it’s not something that needs to be be neutralized by way of sprouting. I’ve seen some gluten-as-antinutrient terminology sprinkled around the otherwise very exacting WAFP site. For example: (scroll down to “OTHER ANTI-NUTRIENTS)
      …and I am highlighting flaws in these popular theories so that we can better understand what the real issues are with gluten so that people will eliminate it for the right reasons and make sure to get the best-quality gluten-containing products if elimination is not necessary.

      So I thank you for bringing this up because I bet others were reading it as you did!

  13. What about the gluten in einkorn? If I eat “normal” wheat I get rashes, very tired, and a stuffy nose and ear ache. After reading that einkorn has a different gluten I tried it and I have no symptoms! But I have been somewhat annoyed that no sources I can find talk specifically about why/how einkorn gluten is different; everything written for the public is dumbed down, but I don’t have access to studies. I really liked that you went into detail in Deep Nutrition so I thought to ask. Thanks!

    1. Celiac is a particularly fascinating topic that I regret not having the space to cover more thoroughly in Deep Nutrition. For that reason I did delve into some pretty geeky detail on this post Particularly of interest to you, and others with acute scientific curiousity, will be the images of the little hexagons and pentagons that impart immune specificity. The issue you are having relates to this specific fingerprinting capacity of the immune system, and the topic is covered in all college level immunology texts which, while not as fun to read as Deep Nutrition 🙂 will help you understand the issue if my aforementioned post doesn’t go as “Deep” as you would like.

    2. In Wheat Belly, Dr. Davis goes into some depth about einkorn (and emmer) wheat, and how it differs from the modern semi-dwarf triticum frankenwheat. I have discussed this with a commercial baker who told me that it is not unusual for a celiac to have extreme reaction to post-1970 frankenwheat and none at all to einkorn or other pre-1970 strains of grain. Dr. Davis also points out that gluten is not the only problem with modern frankenwheat. There are two other new proteins that cause problems.

      1. I have no doubt that there are people who tolerate one epitope on the gluten molecule and react to another. Potentially antigenic epitopes arise during processing, and I don’t believe Dr Davis mentions this (but correct me if I am wrong).

        Perhaps the single most powerful reason some people develop intolerance to gluten is the issue of adjuvant effects that arise when isolated (already processed) gluten is added to sugar and vegetable oil-rich foods and futher processed. I describe this in more detail here.

        1. You might ask him directly. Like me, he also blogs — and is accessible. Next time I see him, I might ask him myself. He is of the opinion that wheat is not suitable for human consumption (and I agree, along with most of the paleo community), and I don’t recall him going into any depth about processing or combinatorial effects on gluten. After all, if you don’t consider it to be food, it doesn’t really matter how you process it. And veggie oils are a problem all by themselves. As is sugar.

          I do recall that Dr. Davis does not consider gluten to be the worst of the problems with frankenwheat, which he mentioned at the presentation I attended in May. I think the video of his presentation is available on the web. If not, I’m pretty sure the DVD is available via Jimmy Moore.

          1. I’ve read Wheat Belly after going grain free (ala Paleo/Primal) and I don’t know what it was about the arguments in book but the way Dr. Davis presented his info in the book actually made me reevaluate my perspective on grains and take the same position as Dr. Cate.

            Due in large part to reading Deep Nutrition and other books/blots I’ve come to the opinion that the worst ‘foods’ are vegetable oils with sugars coming in a distant (but still significant) second.

          2. I found Dr. Davis’ arguments compelling, even though I didn’t change my diet (I have been grain-free since 1999 & much healthier as a result).

            I find fixation about “inflammation” being the root cause of All Bad Things to be strange. Wheat contains 3 proteins that, in concert, compromise the gut lining, causing stuff that should stay in the intestine to cross over to places it doesn’t belong — which *causes* inflammation because the immune system detects foreign compounds, & attacks them.

            Inflammation is merely the immune system’s response to something that shouldn’t be there. The cure is pretty obvious, at least to me, if not Dr. Cate. In celiac, it’s clear that “something” is gluten. In my own case, it’s not clear whether it’s gluten, or some other part of grain, and I’m not even all that interested in finding out, since elimination of grain fixed most of my problems.

          3. From what I understand the problem with inflamation isn’t in and of itself inflamation but the body’s inability to turn off inflamation when it is no longer needed which leads to cronic inflamation.

            I think everything that Dr. Davis has said is bad about wheat is true, and grains in general, however I think it is overstated. If you have a strong body by eating healty fats and remvoing vegetable oils and getting plenty of vitamins and minerals from quality food then the detriment from wheat and other grains are insignificant.

            I think going grain free is a healthy option and would never try to pursuade anyone from altering their grain-free diet. I just think that the anti-grain arguments are a big overblown in general. Also, I’m currently reading The Primal Blueprint and loving it.

  14. I’m a bit irritated with your comment length restriction. I wish to add that my own experience (and that of several others I know) with gluten elimination (even though I’m not celiac) leads me to believe that 1) elimination of all gluten grains should be the first prescribed intervention for nearly any chronic health problem, and 2) failure to do so amounts to malpractice.

  15. I find the arguments in Wheat Belly to be convincing, and the genetic modification (which the Grain Foods Foundation insists isn’t really genetic modification, which relies on a very strained and precise definition of the term — which, BTW, is a reliable indicator of when a politician or corporate shill is deliberately misleading you) of wheat really is a major problem, much more so than the mere selective breeding for things like, say, enhanced fructose content or easier packaging.

  16. I have an auto-immune disease (Devic’s disease) and have been told that I have antibodies and raised white blood cell count. In my mind this sounds like I have chronic inflammation. Should I be avoiding gluten and other pro inflammatory foods? In my case I am unsure adopting a low inflammatory diet will do anything to stop the symptoms related to Devic’s.

    1. While I can’t offer specific medical advise there is every reason to believe that reducing inflammation helps most chronic medical conditions, even those with an underlying genetic basis, because it supports proper operations of the rest of your body functions. Food Rules highlights the inflammation/chronic disease connection in the introductory sections.

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