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Gluten Intolerance is All in Your Head (i.e., Brain)

Gluten Intolerance is All in Your Head (i.e., Brain)
January 17, 2016 Patrick Nemechek, D.O.

Blog GlutenFor many of us, gluten intolerance is “all in our head”.  The key to the problem is silent Autonomic Nervous System dysfunction in our brain.  

Gluten is a protein molecule found in wheat, barley, and rye.  Gluten gives dough elasticity, helping it rise and often gives food a chewy texture. 

Some individuals become sick eating gluten because they have developed an autoimmune disorder in the small intestine called celiac disease that is fueled by gluten in their diet.

Other people notice that cutting gluten out of their diet makes them feel better even though medical tests show they do not have celiac disease.  These people have non-celiac gluten sensitivity.

People blame gluten sensitivity on a condition called leaky gut; medically this is known as increased intestinal permeability.  Gluten is capable of passing through the space between intestinal cells called tight junctions.

When patients with gluten sensitivity eat gluten it leaks through the tight junctions across the gut and triggers an inflammatory reaction.  This causes a host of intestinal and systemic symptoms (cramping, achiness, joint pain, rashes, and fatigue).  But this is not the complete picture.

Studies are now showing that gluten leaks across the gut of all individuals whether or not they have symptoms.  It is just that some people do not develop inflammation to gluten.  So the reality is that we all have leaky gut but not all of us develop inflammation.  The difference lies in the way our immune system reacts to the gluten.

Mechanically, our brain controls our digestion through the Autonomic Nervous System.  The Autonomics control our digestive tract, nutrient storage, bladder control, and gastrointestinal motility.

Interestingly, we are also learning that the parasympathetic and sympathetic branches of the Autonomic Nervous System regulate the immune system as well as the permeability of the tight junctions of the intestinal tract.

In my experience, many patients feel better when they restrict gluten from their diet.  But their real problem is not the gluten causing inflammation; it is the underlying Autonomic damage they have suffered from silent (emotional) or physically traumatic concussions that causes the inflammation.   

And after a few months of treatment designed to restore Autonomic function, my patients not only feel much better in a variety of ways but their gluten intolerance is also gone.  In other words they can enjoy bread, pasta, and beer again.

Symptoms from gluten in your diet are indicative of possible underlying Autonomic damage that is usually repairable.  The answer to fixing gluten intolerance might just be “in your head” where you Autonomics are.

© Copyright 2016.  Dr. Patrick M. and Jean R. Nemechek.  All rights reserved.


  1. Noelle 2 years ago

    Hi Dr Nemechek, we started the modified protocol for anxiety 2 months ago, and started 1/8tsp inulin 10 days ago. My daughter is recently diagnosed with celiac disease and has been commenting on how her stomach feels after the inulin. I wanted to check with you that the inulin is ok for people with celiac disease? Do you know if there is a specific inulin that is better for a person with celiac? Many thanks in advance, NK

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Inulin is compatible with children with Celiac Disease.

      But if there is an issue with inulin that doesn’t resolve within a few weeks, I’d consider treatment with rifaximin as an option especially in this age group.

  2. Krissy 2 years ago

    Hi Dr Nemechek,
    My son is 4 year old ASD, been on the protocol since March 2018. In May he was diagnosed with celiacs disease as well.
    Since he is immune compromised he is constantly sick. I’m aware a healthy gut is key to a healthy immune system and the protocol will build that up. But is there anything that can help boost his immune system along with the protocol? His blood test levels were very high and the specialist advised it could take 2 years or longer before everything normalizes. While he’s making great progress on the protocol, these sick days set him back.
    Looking for any further advise you can give

    • Author
      Patrick Nemechek, D.O. 2 years ago

      The immune compromised state that can accompany celiac disease is more from the inflammatory state that triggers celiac and less from the celiacs itself.

      The protocol helps reverse inflammation-associated immune suppression. You might want to investigate if some of his illness are secondary to chronic sinus/nasal congestion for allergies.

  3. Gaelle ndeou 2 years ago

    Hello Dr Nemecheck ,first of all I would like to thank you and your wife on behalf of my little boy with ASD for making that protocol available for all.therefore I got a concern regarding my little guy and I hope you can help me with son is 4 year old ,severe autistic and non verbal .one of the main cause with started the protocol was because of drooling. He can have like up to 3 shirts change during the day.he got a sinusitis historic .And my occupational therapist is at lost with the drooling .so we have seen an ENT doctor and he prescribed us GLYCOPYRRONIUM,GLYCOPYRROLATE 1 mg/5mL oral solution.My question is do you think my son can take it without having his protocol affected?or do you think with enough time in the protocol ,the drooling issue will be solved? By the way,we are only 2.5 months in the protocol.
    Thanks you so much for your guidance.Have a good day.

    • Author
      Patrick Nemechek, D.O. 2 years ago

      No, those substances will interfere with recovery, and this will ultimately recover.

  4. Kasia Rygalik 2 years ago

    Dear Dr. Nemechek,

    My son has been on your Protocol for one full year and… I’d say he is 90% recovered from Autism! He is 2 years, 8 months old, a sweet, affectionate little boy, sleeps through the night, and is starting to talk. I am forever grateful to you for sharing your Protocol so generously with people around the world. I especially loved the “no special diet necessary part” 🙂 And here is the thing… My son still has digestion issues after all this time on inulin (we worked up to 1 tsp per day) and very little appetite. He will eat a few bites and stop. He gets sudden bouts of diarrhoea (sometimes so bad, I have to change all his clothes AND shoes). We get formed, brown, digested stool max. one day per week. Other times, it is undigested food, not just some particles like tomato skins but everything comes out undigested (especially fruit bits). He does not gain weight, he is 13 kg at 94 cm tall and has been that way for months. Very thin. Also, his immunity is a challenge. He started preschool this year and we are battling a THIRD upper respiratory infection this month… What to do? I thought it was gluten intolerance but now I am lost. Fructose intolerance? Dairy? Thank you!

    • Author
      Patrick Nemechek, D.O. 2 years ago

      The food issues are generally easy to detect.

      I would consider discussing this with a pediatric a=gastroenterologist to be sure there is nothing underlying such as Crohn’s or maybe a true parasitic or enteropathogenic bacterial infections.

  5. ROSANNA 2 years ago

    buenas! tengo muchos síntomas pero lo más desgastante es la fatiga y la hinchazón abdominal, según las pruebas de laboratorio no soy celiaca pero si suprimo el gluten mejoro considerablemente.
    Quiero probar con el protocolo, Tengo 45 años… qué es lo que debo comprar de la tienda? y cómo lo debo iniciar?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I’m sorry I don’t speak Spanish well enough to answer your questions.

  6. Anonymous 2 years ago

    So your protocol doesn’t help with Celiac Disease then? Just Gluten sensitivity?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Yes, that is correct.

  7. sasmita 3 years ago

    Hello Sir,

    Plz help….!!!!!

    16 days on protocol..Imprved a lot..more words,eye contact improved,more engaged,responding to name call
    Dose was – 1/16 inulin, half spoon evoo,dha

    After 10 days given 1/8 in morning and 1/16 in night..for 2 days..did not see any much changes…Introduced MB12 as she was having deficiency

    After 2 days increased the inulin dose to 1/16 morning, 1/16 afternoon,1/8 dinner.
    Due to teeth grinding given neem + turmeric 2 times a day suspecting worms

    From last 3 days..seeing regression…eye contact has decreased,not seeing the mastered words, no new words, lot of meltdowns,totally lost…in her world..not responding to name call..sometimes unusual laughing….

    what could be the issue…Should I decrease to the previous dose..or some other issue..

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Things sounded as if they were going fine when the dose was – 1/16 inulin, half spoon evoo, dha.

      Go back to that dose and stop the additional supplements. Obviously one of them was causing the problem.

  8. Bayyinah Muhsin 3 years ago

    Do you treat children with your Autonomic Brain-Nerve treatment plan? My 5 year old has been diagnosed with autism. He has been on your protocol for 4 months now and we see the improvements you speak about.

    The problem is he has developed extreme constipation. We think it might be gluten intolorence. What do you suggest? He is not adverse to taking the fish oil. Should we increase it?

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I would just wait and give things more time to recover.

  9. Victoria 3 years ago

    Dr. N,

    Upon consuming Gluten, my stomach immediately (within a couple to 15 minutes) blows up like a football and is very painful. I get severely ill for at least the next 3-5 days after too, all due to my nervous system going into an acute stress response on day 1. I’m being referred for Gluten Ataxia to be investigated due to the longer term symptoms caused but one thing no-one can explain to me is why, a particular type of food allergy medication works so well at stopping this 5 day chain reaction from progressing, if taken early enough (before my stomach inflames past a particular point and/or when my digestive function temporarily shuts down). I didn’t think Gluten Intolerance should be impacted by allergy tablets? Why do they work so well for me? I’m not the only one with these neurological symptoms to report this either. I’ve come across a few others along the way too.

    My symptoms during this 5 day cycle are incredibly consistent and long-standing so it is clear that the trigger is gluten/other wheat protein.

    Any insight you can offer on this query Dr. N, would be more than gratefully appreciated.

    Thank you!


  10. poorna 3 years ago

    My daughter is autistic and will complete her 9 yrs in April 2017. How can we use lnulin and fish oil pls suggest.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      The details are in the post and read some of my blog comments for additional information

  11. Kerri Martin 4 years ago

    I have a gluten intolerance. It’s so bad that I get extremely bloated and gassy.

    • Author
      Patrick Nemechek, D.O. 4 years ago

      Other than seeing me so we can fix your autonomic nervous system, there is not much more you can do other than strictly avoid gluten.

      If you are still having problems in spite of doing that you may have SIBO or what you are experiencing is from the underlying autonomic dysfunction. Autonomic dysfunction is difficult to fully reverse on your own.

      Dr. N

  12. Julia French 4 years ago

    This kind of attitude has caused me much pain and migraines throughout my life. I am 66 years old and just got my labs back saying I have Celiac Disease. Please stop saying that Gluten Intolerance is all in your head! The proper thing is say is to GET TESTED!! Thank you

    • Author
      Patrick Nemechek, D.O. 4 years ago


      A careful reading of the article will show you I do take the issue of physical reactions to gluten seriously, and I discuss the underlying mechanisms coming from the brain that are responsible for the reactions to gluten. I also specifically state this article does not apply to those with Celiac Disease.

      I’m glad for you that your were finally properly diagnosed.

      Dr. N

  13. Rachel Tallman 4 years ago

    Hi I have these symptoms of gluten intolerance. They developed before my colon cancer diagnosis four years ago or more, as I have had stomach discomfort of bloating and constipation for many years. I have retained these symptoms since my partial collectemy surgery, three years ago. I found eliminating gluten from my diet has significantly helped. I am now cancer free after the removal of 20 cms of my colon. I live a “normal” life and am very grateful that my cancer was found before it had metastasized and that I did not require chemotherapy. I am very curious what is your therapy that could return me to a life without gluten sensitivity.
    I actually found your website as I was doing more research for my daughter who has been diagnosed with autonomic dysfunction. She has frequent “dizziness” that has resulted in her passing out many times in her life. She is seventeen years old and has fainted due to the sight of her blood, extreme panic, being overheated, physical pain, hormone changes (birth control pill), and emotional difficulty. I am very interested in any therapy that could help her live a normal life again, without the fear of passing out.

    • Author
      Patrick Nemechek, D.O. 4 years ago

      The gluten intolerance is from a combination of bacterial overgrowth (SIBO) and underlying autonomic dysfunction. Most autonomic dysfunction seems to be from inflammatory and/or traumatic damage to the nervous system; damage that should of been repaired but couldn’t be because of underlying metabolic inflammation. Excluding people with true Celiac Disease, gluten sensitivity is an abnormal inflammatory reaction to gluten that “leaks” into the mesenteric tissue surrounding the gut – this seems to be specifically due to parasympathetic damage and improves greatly, especially with vagus nerve stimulation.

      To reverse autonomic damage, I lower metabolic inflammation through a multifaceted approach that reverses SIBO, blocks the damaging effects of linoleic acid and then uses high dose DHA along with vagal nerve stimulation to further suppress the damaging effects of activated microglia within the brain. go to and watch the screencast on metabolic inflammation and maybe the one on vagus nerve stimulation and olive oil to get a full idea of the approach.

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