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Coffee should be avoided by those who are Celiac and many who suffer from wheat sensitivity as it contains cross-reactive proteins to gluten.

If you drink coffee, even bulletproof coffee and have gluten sensitivity or celiac, you might want to sit down for this one.
There is a surprising connection between gluten and coffee that is by and large ignored by the health community. This revelation holds ramifications for other autoimmune disorders as well.
The problem has nothing to do with caffeine, so decaf coffee would be included in this discussion.
In a nutshell, fairly recent lab research has revealed that 10% of coffee is a protein that cross-reacts with gluten antibodies.
This means that if you are gluten sensitive or celiac and are avoiding gluten-containing grains or perhaps have even gone completely grain-free if you still drink coffee there is a strong likelihood that the protein in the coffee is triggering the very same gluten-related health problems you are trying to avoid.
In other words, even if you think you are doing fine with your current gluten-free diet, it is very possible that skipping the coffee could take your health to the next level.
Symptoms of Gluten Sensitivity
Most people who are gluten sensitive don’t realize it because gastrointestinal problems like burping, gas, tummy upset, or toilet issues are the least common way for gluten issues to present themselves!
The most common symptoms of gluten sensitivity?
Migraines and other neurological issues – even MS!
Hormone and endocrine problems are another common way for gluten issues to manifest themselves.
How Coffee Triggers Gluten Sensitivity
So what exactly happens when a gluten sensitive person eats gluten?
Folks with gluten antibodies react to any gluten in the diet by mounting an immune response. This means that gluten is perceived by the body as an invader and the gluten antibodies attack the gluten itself trying to destroy it.  This gluten attack is an inflammatory response and inflammation issues can occur anywhere in the body in any tissue or organ.
Here’s the real shocker I came across when researching the coffee/gluten connection:
According to Dr. David Clark DC, functional neurologist and endocrinologist:
There’s not a disease or health condition you can think of that does not have an association – in the research literature – with gluten sensitivity.
That’s a very strong statement!
In essence then, if you are gluten sensitive in any way shape or form, and it seems that most people are whether they know it or not given the epidemic levels of autoimmune issues today, gluten antibodies have the potential to react to proteins in other foods as if they are gluten thereby triggering an immune and inflammatory response.
The protein in coffee is the most common cross-reactor for gluten. Because it is the protein in the coffee that is the trigger, switching to decaf coffee does not solve the problem. Apparently, instant coffee is the worst offender.
Is it possible to be gluten sensitive and not cross-react to coffee? Yes, it’s possible but you’ll have to do some expensive lab testing with a knowledgeable doctor to find out.

Reference
Journal of Food and Nutrition Sciences
More Information
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Coffee Enema
Morning Coffee Fix
Caffeine and Chronic Back Pain
Healthy Coffee Substitutes
@Jim, for you but not all people!
Oh my God how do I get off the response to this coffee thing and gluten. This is a HOT topic and I would like to know how to STOP receiving comments on it. Any Help?! Or I am gonna grab a cup of JOE!
thank you
coffee is just a state of mind I think…because it tastes like crap!! I drink it about 10 times a year,with lots of flavored creamer
Gosh, what else are they gonna take away from me???
I find this extremely disturbing.
wahhhh!!
wahhhh!!
So phooey on this news. Had heard part of reason to avoid beans on paleo is gluten, maybe that’s a bean thing.
I too felt great at first on Paleo – stabilized my wicked blood sugar problems – then got so tired I couldn’t function. On more carbs now and feel much better. Am being very careful with which ones because my gut still isn’t healed all the way. For example, after adding back gluten free oatmeal, some bad neurological issues came back after being completely gone while grain free. So am looking for the optimal mix of grain-free (for blood sugar, gut healing, and neurological stuff) and the right level of carbs (for energy and my thyroid). And, if this is really true about coffee (hey – maybe it isn’t!), it’s either drink coffee or get my life back. Hmmm…..wonder which I’ll choose.
I heard a lot about gluten intolerance but I had never heard of Gluten Ataxia, an autoimmune disease that attacks your brain. It’s pretty rare. Worst of all, it’s likely that most of the doctors are clueless about it, even though simply go gluten free will stop the attack and lead a normal life.
http://www.livingwithout.com/issues/1_11/untreated_gluten_sensitivity-1800-1.html?ET=livingwithout%3Ap76216%3A223054a%3A&st=pmail&s=P_TuesdayTip100212&t=B_TL_P