top of page

The Real Reason You are Still Sick with Celiac: What Your Doctor Won't Tell You

You’ve been diagnosed with Celiac Disease.

It’s been a year gluten-free, or maybe much longer.

Like me, you were promised that the gluten free diet would be the magic bullet back to health, but what if it isn’t?

What if, despite being 100% gluten free, you are still sick? Or what if you have new symptoms since going gluten free?

What if you still have bloating, gas, diarrhea/constipation, weight gain/weight loss, brain fog, numbness or tingling in strange places, joint pain, random swelling, or fatigue that you just can’t shake, no matter how much sleep you get- or are you riddled with insomnia, no matter what you do?

I bet you’ve gone to your doctor, looking for answers as to why you still feel sick. I bet you’ve asked, or is it begged, for tests to find out what is going on and likely received little clues. Maybe your retests for anti-tTG and anti-endomysium look normal… congratulations, you’ve healed! But what if you don’t feel normal?

Or, maybe your blood tests are still elevated or your endoscopy is still showing damage, no matter how strict you are on the gluten-free diet.

Then what?

Well, the reality is, Celiac is an autoimmune disease. We all KNOW that, but sometimes Celiac gets placed into its own category because there is a plan for getting better…. the gluten-free diet.

But what about your gut? Will it heal simply in the absence of gluten?

What about your immune system? Will the inflammation stop?

What if you have brain fog, brain inflammation or ataxia? Will it get better on its own?

What if you have other autoimmune diseases? Will they get worse?

Or, what if you are worried about getting more autoimmune diseases because you know you have a 25% increased risk?

If you look at the medical literature, it is clear there is a sizeable population of Celiacs that continue to have damage to the intestinal villi and heightened inflammation long after gluten has been removed.

At the Bold Beyond Celiac Symposium in November, 2017, the panel consensus agreed, “up to 50% of Celiacs show ongoing or intermittent Celiac activity while on the gluten free diet and more than 30% of adults Celiacs continue to have intestinal damage 4 years after going gluten free”.

4 years!

Here’s what other research tells us:

Complete recovery of intestinal mucosa occurs very rarely in adult coeliac patients despite adherence to gluten-free diet. (1)

Yet, their blood markers were normal.

Persistent Intraepithelial Lymphocytosis in Celiac Patients Adhering to Gluten-Free Diet Is Not Abolished Despite a Gluten Contamination Elimination Diet.

Or here, this research examined two groups at 12-18 months after adopting a gluten free diet. Each participant had a set amount of intestinal damage (Marsh II, grade A lesions). One group ate a Gluten Contamination Elimination Diet (GCED), and one group ate their normal gluten-free diet. Despite a Gluten Contamination Elimination Diet (GCED), there was no change in intestinal biopsy results in either group. (2) It begs the question, is it possible to heal simply in the absence of gluten exposure?

It’s also clear that the typical follow up with anti-tTG and anti-endomysial antibody blood tests is not sufficient, as shown in this research roundup, below.

Tests for Serum Transglutaminase and Endomysial Antibodies Do Not Detect Most Patients With Celiac Disease and Persistent Villous Atrophy on Gluten-free Diets: a Meta-analysis.

”In a meta-analysis of patients with biopsy-confirmed celiac disease undergoing follow-up biopsy on a GFD, we found that tests for serum tTG IgA and EMA IgA levels had low sensitivity (below 50%) in detection of persistent villous atrophy. We need more-accurate non-invasive markers of mucosal damage in children and adults with celiac disease who are following a GFD.” (3)

This indicates the current testing is not catching people who have ongoing intestinal damage and inflammation. Basically, it is not helping Celiacs who are eating gluten free and not getting better, putting us at risk for other autoimmune diseases, other diseases, in general, cancer and even death.

Additionally, in Celiac, it is not uncommon for Zonulin, the gatekeeper hormone that decides what is allowed through the cells of the epithelium, to remain high, contributing to gut permeability or “leaky gut”, long after gluten has been removed. High Zonulin is associated with developing other autoimmune diseases as well as increasing your risk for obesity, high cholesterol, insulin resistance, and metabolic syndrome, among others. (4)

You may have heard of Refractory (RCD) or Nonresponsive Celiac Disease (NCD) and are thinking, “well, I haven’t been diagnosed with that and anyway, it’s really rare”. Well, I believe that our lackluster follow up testing has made that disease rare and I think that many more Celiacs are suffering from continued damage from Celiac Disease and the gluten free diet just won’t suffice. The problem lies in our medical community who are not educated into the nuances of Celiac. If you go to your doctor or Mayo Clinic, complaining of continued symptoms, you are likely to be brushed off because they believe you must be cheating on your gluten-free diet. End of story.

I’m here to tell you today, that, even in the absence of Refractory or Nonresponsive Celiac Disease, you still have symptoms- or have NEW symptoms because:

1. Simply removing gluten will not necessarily heal your gut or calm the chronic inflammation associated with all autoimmune diseases. 2. There is an autoimmune inflammatory process raging through your body and it won’t subside on its own. 3. You are eating foods that you are either sensitive to or are similar enough to gluten and those foods are triggering inflammation and symptoms. 4. You have not addressed what caused Celiac, in the first place.

You see, you need to investigate why you developed an autoimmune disease, in the first place.

OK. Let’s assume you’ve already checked your food and environment for cross-contact. You’ve already thrown away your cast-iron skillet, scoured all ingredient labels, you have a dedicated gluten-free toaster and cutting board, you only eat certified gluten-free food, you’ve switched out your body care products to gluten-free versions, you’ve checked and double checked your prescription and over the counter medications, etc. etc.

AND you’re still sick…

Top 5 contributors to continued symptoms after Celiac diagnosis:

Here’s what you need to do to heal your body and get better:

1) Eliminate all packaged, processed gluten-free “food”:

You cannot eat gluten free pretzels, donuts, pizza, cookies, crackers, bread, cake, candy and chips and expect to feel good. Gluten-free junk food is like junk food on steroids. It contains hyper-processed starchy flours that don’t have any nutrition and disrupt your gut flora, blood sugar and health and cause inflammation.

Many gluten-free junk foods contain GMO’s, high levels of glyphosate, carrageenan, guar gum, xanthan gum, corn, high amounts of sugar and fake flavors. Even Certified Gluten-Free packaged products are allowed to have between 5 ppm and 20 ppm gluten, depending on the organization doing the certifying. Do some math and you will see how the amount of gluten you are eating adds up when you eat multiple servings of these foods each day. These ingredients contribute to gut dysbiosis, yeast overgrowth, inflammation, high blood sugar and gut damage. You cannot expect to eat these “hyper-processed” foods and feel good, plus many gluten-free junk foods contain highly allergenic or gluten-cross reactive ingredients (see below).

2) Check for mineral and vitamin deficiencies.

Since you’ve likely had years of blunted villi, crypt hyperplasia, and “leaky gut” (gut permeability) you are likely deficient in vitamins and minerals. Plus, if you are still feeling sick, it’s possible you are still in a state of malabsorption.

Check iron levels, Vitamin D (25 Hydroxy AND Vitamin D 1, 25 OH, Calcitrol), calcium, magnesium, folate (especially if you have MTHFR), zinc, niacin, riboflavin and B12.

Less commonly, you might have a copper deficiency (or toxicity) and B6 might be low, especially if you are prone to infections, have anxiety or have numbness or tingling anywhere on your body.

Be aware that the usual testing for vitamin deficiencies in blood is futile. Blood is tightly regulated by our body out of survival. Deficiencies will only show up years later when the body can no longer cope. So, again, you won’t feel well, but your blood test might look “normal”. I prefer Functional Testing such as Hair, Tissue Mineral Analysis or Vibrant America’s Micronutrient Test that looks at extracellular AND intracellular nutrients.

3) Eliminate gluten cross-reactive foods and other foods you are sensitive to because they are causing damage to your gut, adrenal exhaustion and inflammation:

Many foods such as dairy, some GF grains (millet, rice), yeast and oats can act like gluten in your system. When you eat these foods, your body is making antigens to different tissues in your body. The protein structure of these foods is similar enough to gluten that it will continue the inflammatory response.

You are probably thinking, “yea, but when I eat those foods, I don’t get 'glutened'”.

Yep. You are right. You won’t feel glutened by these foods because they don’t contain gluten. But, they still cause inflammation and symptoms because the protein structure is similar enough to gliadin and, to make matters worse, your immune system might be mounting an attack on self-tissue, such as your cerebrum, other neural cells, liver cells, pancreatic cells, and adrenal cells. (5)

I suggest either using Cyrex Test Array #4 and testing to see if these foods are a problem or switching to the Autoimmune Paleo Diet. This diet is anti-inflammatory, low lectin, low in phytic acid, agglutinin, prolamines and naturally removes most of the highly allergenic and gluten cross-reactive foods, with a few exceptions. If you’ve ever eaten something and felt “kind of glutened”, but it was slightly different, it’s highly likely you have other foods causing reactions.

In addition to the Gluten Cross-Reactive foods, other foods might cause symptoms because you are sensitive to them- not an allergy, but a sensitivity. Foods like corn, soy, nuts, peanuts, night shades (tomato, potato, peppers, etc.), high oxalate foods (spinach, swiss chard, quinoa, sweet potato, etc.), grains, chicken, fish, or even garlic can cause delayed reactions that might happen hours or days after you've eaten the food. These foods will not cause anaphylaxis, but will keep you in a state of not feeling well and can further damage your gut.

4) Check for hormonal imbalances: thyroid, thyroid antibodies, adrenals and sex hormone levels:

You might be thinking, “yep, my doctor said my TSH is normal”. Well guess what? Checking only TSH (thyroid stimulating hormone) will not give you a true picture of thyroid health. TSH tests the communication between your brain and thyroid gland, not how much thyroid hormone you are making or how much thyroid hormone is in its active form. TSH can look normal for years and years, but you don’t feel normal!

In addition to TSH, you need to ask your doctor to run total T4, total T3, free T4, free T3, reverse T3, TPO antibodies and Thyroglobulin antibodies. In addition to running these tests, it is wise to look up functional values or ranges for these tests. The range your doctor uses is very wide. The people at the top and bottom range of “normal” will have symptoms and show the early signs of imbalance. Functional Interpretation looks at the narrow range that represents a healthy person and addresses the people who don’t feel well, but might be considered normal by medical standards.

According to Dr. Izabella Wentz and Dr. Datis Kharrazian, roughly 90-97% of people with hypothyroidism have Hashimotos (an autoimmune thyroid condition where your body is attacking your thyroid). Many doctors don’t check for antibodies because there is no medical treatment for it (meanwhile thyroid tissue is being destroyed by your immune system and you might not even know!), yet there is much to be done in the realm of nutrition, decreasing stealth infections (EBV, gut infections), decreasing toxic burden, etc. to stop the autoimmune thyroid attack.

One study by Melo et al. showed the co-occurrence of Hashimotos with anti-endomysial antibodies is increased 5 fold, while the co-occurrence of Hashimotos with anti-tTG antibodies is increased by more than 3-fold. (5)

What about estrogen dominance? Low progesterone? High or low testosterone? Cortisol?

Every hormone in your body is interconnected and has a profound effect on how you feel. If your thyroid is off, so are your stress and sex hormones. Additionally, when your body is under stress, it will protect itself by dialing down hormone production, essentially "putting on the brakes".

Again, blood is not the best way to test. Urine metabolites or saliva is much better.

5) Check for infections and dysbiosis:

There is ample research linking early Rotavirus, Campylobacter, Adenovirus (Parainfluenza), Hep-C infections to increased Celiac risk in susceptible individuals. (7, 8, 9)

Unfortunately many medical professionals don’t recognize the link between other common “stealth” infections and Celiac and autoimmunity, in general, because they are 18 years behind the current research. For instance, in my practice, I see gut infections such as Roundworm, Whipworm, Blastocystis hominis, Cryptosporidium, Giardia, or Candida often. Research shows that bacteria such as H pylori, Yersinia, Klebsiella, Citrobacter and Mycobacterium terbuculosis can cause autoimmunity. The presence of these infections alters the gut microbiome, causing nutrient deficiencies, continued gut discomfort, malabsorption inflammation and are a source of ongoing toxic burden on your body and brain. I see time and time again, when these infections are addressed, the auto-antibodies decrease, your gut can heal, the inflammation subsides, brain fog goes away and you feel better.

The role of infectious mediators and gut microbiome in the pathogenesis of celiac disease.

“It is possible that sensitivity to gluten increases in patients infected with infectious diseases, and consequently infection may trigger CD in susceptible individuals. It is likely that, due to reduced immunity following the loss of intestinal villi, viral, bacterial, and parasitic infections develop faster in celiac disease patients and systemic complication occur more frequently.” (10)

With Hashimoto’s, there is a strong association between reactivation of Epstein Barr Virus and autoimmune thyroid disease, as well as infection with Blastocystis hominis (parasite). There is debate as to whether your immune system has gone rogue and is attacking self-tissue through molecular mimicry or whether your immune system is doing what it is designed to do and is going after the infection (EBV in thyroid tissue, for instance). In the latter, self-tissue is the bystander getting destroyed in the normal immune process.

It is also necessary to check for dysbiosis where the normal bacteria in the gut has overgrown or colonic bacteria has migrated to the small intestine, causing SIBO. Normal, healthy bacteria are necessary for our survival... literally! We depend on the bacteria in our gut to digest our fiber and manufacture vitamins, among so many other things. In the right amount, they are anti-inflammatory and actually tell our immune system what to do. But, when they overgrow, they become pro-inflammatory and can cause problems such as gas, bloating, brain fog, anxiety and depression. SIBO (small intestine bacterial overgrowth) causes widespread symptoms such as bloating, gas, brain fog, dizziness, constipation/diarrhea, food sensitivities and hundreds more. SIBO is common in Celiacs who don’t feel better on a gluten free diet- studies show somewhere between 9% and 66% of Celiacs have SIBO. (11,12)

If you have a worm, parasite or bacterial infestation, Candida will follow along. Yeast overgrowth is opportunistic, so when the microbiome has been disrupted, yeast will overgrow, again causing symptoms such as brain fog, rashes, fatigue, fungal infections of the nails, skin or vagina, increased food intolerances, sugar and carbohydrate cravings and more.

So, the question remains, is your gut microbiome healthy or is it causing more inflammation and nutrient deficiencies because it never healed? We are just beginning to scratch the surface when it comes to the gut microbiome. What we do know is this, the balance of flora will dictate whether or not you have depression, anxiety, inflammation, infections like SIBO, a yeast overgrowth, allergies, mental disorders, malabsorption, reflux and the list goes on and on. I don’t think there is a symptom that cannot be linked to poor gut health.

If you’ve already investigated all of the aspects mentioned above and are still feeling sick, it’s time to move on to advanced investigation of mold illness- CIRS (Chronic Inflammatory Response Syndrome), vector-born illness such as Lyme and Coinfections, toxicity (plastics, preservatives, glyphosate, heavy metals, fluoride, bromide, etc.), Kryptopyrrole or genetic SNP’s.

If you want more information, want to take charge of your health or are desperate for answers, contact me to schedule a free 30 minute consultation and find out if I can help you. I work one on one with clients to uncover the root of your illness.

Allana McKinnon, FDN-P is not only highly trained in Functional Health Practices, she has lived through chronic illness and reversed her own Celiac Disease and other health challenges such as asthma, allergies, hypothyroidism, a half dozen gut infections, and CIRS from mold and Lyme. She is a Certified Functional Diagnostic Nutrition Practitioner with additional training in histamine intolerance, hyperoxaluria (oxalate metabolism issues), Celiac Disease, detoxification, hormone balancing, SIBO, the Autoimmune Paleo Diet, the microbiome and stealth infectious disease. She will help you determine what lab tests will best illuminate why you feel sick and what actions to take to feel better. She will then guide you toward better health by eliminating the factors creating the loss of function, putting meaningful lifestyle interventions in place, homing in on the right diet for you and working to unblock the physical and emotional factors that led to poor health. Many of Allana's clients enjoy working with her because they feel truly understood, truly heard (often for the first time in their life), they feel she is compassionate and that Allana provides her clients with the answers they are so desperately seeking.


(1) Lanzini A, Lanzarotto F, Villanacci V, Mora A, Bertolazzi S, Turini D, Carella G, Malagoli A, Ferrante G, Cesana BM, Ricci C. Complete recovery of intestinal mucosa occurs very rarely in adult coeliac patients despite adherence to gluten-free diet. Aliment Pharmacol Ther. 2009 Jun 15;29(12):1299-308. doi: 10.1111/j.1365-2036.2009.03992.x. Epub 2009 Mar 3. PubMed PMID: 19302264. (2) Zanini B, Marullo M, Villanacci V, Salemme M, Lanzarotto F, Ricci C, Lanzini A. Persistent Intraepithelial Lymphocytosis in Celiac Patients Adhering to Gluten-Free Diet Is Not Abolished Despite a Gluten Contamination Elimination Diet. Nutrients. 2016 Aug 26;8(9). pii: E525. doi: 10.3390/nu8090525. PubMed PMID: 27571100; PubMed Central PMCID: PMC5037512. (3) Silvester JA, Kurada S, Szwajcer A, Kelly CP, Leffler DA, Duerksen DR. Tests for Serum Transglutaminase and Endomysial Antibodies Do Not Detect Most Patients With Celiac Disease and Persistent Villous Atrophy on Gluten-free Diets: a Meta-analysis. Gastroenterology. 2017 Sep;153(3):689-701.e1. doi: 10.1053/j.gastro.2017.05.015. Epub 2017 May 22. Review. PubMed [citation] PMID: 284581 PMCID: PMC5738024. (4) Moreno-Navarrete JM, Sabater M, Ortega F, Ricart W, Fernández-Real JM. Circulating zonulin, a marker of intestinal permeability, is increased in association with obesity-associated insulin resistance. PLoS One. 2012;7(5):e37160. doi: 10.1371/journal.pone.0037160. Epub 2012 May 18. PubMed PMID: 22629362; PubMed Central PMCID: PMC3356365.

(5) Melo FM, Cavalcanti MS, Santos SB, Lopes AK, Oliveira FA. Association between serum markers for celiac and thyroid autoimmune diseases. Arq Bras Endocrinol Metabol. 2005 Aug;49(4):542-7. Epub 2005 Oct 19. Portuguese. PubMed PMID: 16358083. (6) A. Vojdani and I. Tarash, Cross-Reaction between Gliadin and Different Food and Tissue Antigens, Food and Nutrition Sciences, Vol. 4 No. 1, 2013, pp. 20-32. doi: 10.4236/fns.2013.41005. (7) Stene L, Honeyman M, Hoffenberg E, Haas J, Sokol R, Emery L, Taki I, Norris J, Ehrlich H, Eisenbarth G, Rewers M. Rotavirus Infection Frequency and Risk of Celiac Disease Autoimmunity in Early Childhood: A Longitudinal Study. The Americal Journal of Gastroenterology. 2006, pp.2333–2340, doi:10.1111/j.157241.2006.00741.x (8) Troncone, Riccardo; Auricchio, Salvatore. Rotavirus and Celiac Disease: Clues to the Pathogenesis and Perspectives on Prevention. Journal of Pediatric Gastroenterology and Nutrition: May 2007 - Volume 44 - Issue 5 - p 527–528. doi: 10.1097/MPG.0b013e31804ca0ec (9) Plot L, Amital H. Infectious Associations of Celiac Disease. Autoimmunity Reviews: Volume 8, Issue 4, February 2009, Pages 316-319. (10) The role of infectious mediators and gut microbiome in the pathogenesis of celiac disease. Rostami Nejad M, Ishaq S, Al Dulaimi D, Zali MR, Rostami K - Arch Iran Med - April 1, 2015; 18 (4); 244-9 (11) Tursi A, Brandimarte G, Giorgetti G. High prevalence of small intestinal bacterial overgrowth in celiac patients with persistence of gastrointestinal symptoms after gluten withdrawal. Am J Gastroenterol. 2003 Apr;98(4):839-43. PubMed PMID: 12738465. (12) Rubio-Tapia A, Barton SH, Rosenblatt JE, Murray JA. Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. J Clin Gastroenterol. 2009 Feb;43(2):157-61. doi: 10.1097/MCG.0b013e3181557e67. PubMed PMID: 18719514; PubMed Central PMCID: PMC2643326.

Featured Posts
Recent Posts
Search By Tags
Follow Us
  • Facebook Basic Square
  • Twitter Basic Square
  • Google+ Basic Square
bottom of page