top of page

Celiac Disease: A Functional Nutrition Approach

Celiac Disease is the first autoimmune condition identified where the environmental trigger and the primary genetic markers have been clearly defined in the medical literature.

It has also been the disease that has brought to light how gluten, the family of proteins found in wheat, barley, rye and a few other less common grains, can affect the human body.

Unfortunately, there are many people living with Celiac Disease who have either not been diagnosed or who are still struggling with chronic symptoms despite a strict gluten-free diet.

In this article, we will look at the epidemiology and etiology of Celiac Disease along with the risk factors, assessment and interventions from both a conventional and functional perspective with the hope of shedding light on why chronic symptoms may still persist despite a gluten-free diet, and what nutritional interventions can help those who have not found complete resolution of their Celiac symptoms.

Epidemiology & Etiology

Celiac Disease is an autoimmune condition that affects approximately 1% of the U.S. population, however 97% of people with Celiac Disease are not aware they have the disease. (1-2)

Medical research has shown that Celiac Disease can develop in genetically susceptible individuals when the immune system attacks the enterocytes (cells) of the small intestine leading to villous atrophy (flattening) in the presence of the gluten family of proteins found in wheat, barley, rye and a few other less common grains. (3)

Researchers have identified two primary genes associated with Celiac Disease, HLA-DQ2 and HLA-DQ8.

In their retrospective analysis, Cecilio and Bonatto found that 98.4% of people with Celiac Disease carry these human leukocyte antigens. (4) In other research, it has been reported that greater than 95% of patients with Celiac Disease have the HLA-DQ2 or HLA-DQ8 genes. (5)

According to the Celiac Disease Foundation, 25-30% of the general population also carry at least one of the two HLA genes for Celiac Disease, but only 1% of the general population develops the disease. (6)

It is rare, but important to note that it is possible for someone to develop Celiac Disease and not carry either the HLA-DQ2 or HLA-DQ8 genes. (7)

Risk Factors

If approximately 30% of the population carry the genes for Celiac Disease, and the primary environmental trigger is gluten, which most Americans eat, then why do only 1% develop the disease?

To help us answer this question we can look to the work of Dr. Alessio Fassano, M.D. and his team of researchers. In their 2009 manuscript, Visser and Rozing, along with Dr. Fassano, et al., discuss that “There is growing evidence that increased intestinal permeability plays a pathogenic role in various autoimmune diseases including CD [Celiac Disease] and T1D [Type I Diabetes].” (8)

From Dr. Fassano's research we learn that 3 factors must occur for an autoimmune disease like Celiac Disease to develop: (8)

1) genetic susceptibility

2) environmental trigger(s)

3) increased intestinal permeability

Other risk factors that have been associated with Celiac Disease include dysbiosis of the gut microbiota, family history of Celiac Disease, duration of infant breastfeeding, gastrointestinal viral exposure (especially during childhood) and adenovirus type 12 exposure “because the virus has a protein similar in structure to alpha-gliadin”. (9-12)

In my opinion, it appears that the development of increased intestinal permeability, combined with a compromised immune system, and subsequent loss of oral tolerance, might be the determining risk factors between someone who carries the genes for Celiac Disease and consumes gluten, but doesn’t develop the disease vs. someone who does develop the disease.


Common symptoms associated with Celiac Disease include gastrointestinal symptoms such as chronic diarrhea, chronic abdominal pain, malabsorption, bloating, IBS-like symptoms, constipation, failure to thrive, weight loss, anorexia, vomiting, GERD; and extra-intestinal symptoms (outside of the gut) such as iron-deficiency anemia, nutritional deficiencies, fatigue, short stature, delayed puberty, amenorrhea, dermatitis herpetiformis, osteopenia/osteoporosis, dental enamel hypoplasia, and peripheral neuropathy. (13)

When the immune system attacks the villi of the small intestine, as it does in the case of Celiac Disease, antibodies against the tissue transglutaminase-2 (t-TG2) enzyme are produced. This autoimmune attack destroys the villi (finger-like projections that absorb nutrients and release enzymes) of the enterocytes (cells lining the digestive tract).

The gold standard for diagnosing Celiac Disease is a biopsy of the duodenum (beginning part of the small intestine just past the stomach) and then analysis of the tissue to determine the degree of villous atrophy that has occurred.

The tissue collected from the biopsy is analyzed and assigned a Marsh Classification. A Marsh rating of 0, 1 or 2 indicates normal tissue. (14) A Marsh rating of 3a to 3c indicates mild to complete villous atrophy. (12)

When tissue is viewed under a microscope, the villi should look like "shag carpet" (see picture below). In the case of total villous atrophy like in advanced Celiac Disease, it looks more like "berber carpet", smooth and rounded instead of finger-like projections extending from the outer layer of the enterocytes.

A serum blood test is an easier, less invasive way to screen for Celiac Disease because it can check for elevated antibodies to t-TG2. (12)

Immunoglobulin-A (IgA) and immunoglobulin-G (IgG) antibodies can be produced against t-TG2, so in my opinion, it’s best to check for both IgA and IgG antibodies to t-TG2 when utilizing serum blood testing to assess and monitor someone with Celiac Disease.

Oftentimes, conventional medicine will only check for IgA antibodies to t-TG2. This is problematic for two reasons. One reason is because someone may be deficient in the production of secretory IgA, and if that is the case, then their serum IgA antibody test would likely produce a false negative result. (15) And secondly, if someone has elevated IgG antibodies to t-TG2, but not elevated IgA antibodies, and only IgA is tested, then it’s possible to miss a proper diagnosis, which could result in someone leaving their doctor’s office thinking it’s okay to continue eating gluten.


There is no cure for Celiac Disease, and complete, 100% avoidance of gluten is the only treatment available. However, additional interventions widely recognized in the medical community that have shown to help with Celiac Disease include: correction of nutritional deficiencies and the avoidance of dairy, especially if there is also lactose intolerance. (16-17)

Nutritional deficiencies are common in Celiac Disease due to the reduced surface area and brush border enzyme production because of the destruction of the intestinal villi.

Nutritional deficiencies commonly associated with Celiac Disease include: “B9, B6, B12, iron, zinc, calcium, copper, fat-soluble vitamins like A, D, E, and K, and dietary fiber.” (16)

Lactose intolerance is common in Celiac Disease due to the reduced production and release of lactase from damaged enterocytes. (17) Lactase is a brush border enzyme that helps to break down the milk sugar, lactose. When the villi are damaged, they are no longer able to produce and release lactase efficiently leading to gas, bloating and abdominal discomfort when someone consumes foods or liquids high in lactose like cow's milk and ice cream.

Increased intestinal permeability has also been shown to persist even on a gluten-free diet. (16)

This may be due in part to the dysbiosis of the gut microbiota that has been shown to be associated with pathogenesis of Celiac Disease. (18) Avoiding gluten helps to reduce inflammation and intestinal permeability, but a gluten-free diet alone is typically not enough to restore balance to the gut microbiome. Unfortunately, this is not something commonly recognized and addressed in conventional medicine.

However, Functional Medicine and Functional Nutrition are uniquely positioned to be able to help people living with Celiac Disease more comprehensively identify and address the underlying root cause imbalances which may be persisting even after the implementation of a gluten-free diet.

One of the tools to help rebalance the gut microbiome and improve gut barrier function that has been researched and reported in the medical literature is the use of probiotics. The following strains of probiotic bacteria have been shown to be helpful in Celiac Disease: Bifido. infantis, Bifido. longum, Bifido. breve, and Lactobacillus casei, and Lactobacillus plantarum. (19-23)


One of the pitfalls of a gluten-free diet is the consumption of highly processed gluten-free substitute foods that are filled with refined carbohydrates and sugar.

It’s wonderful that there are gluten-free versions of just about every food made with wheat, however most of these foods are not considered nutritious and may come with unintended consequences.

Theethira and Dennis discuss in their 2015 article that “Weight gain and obesity have been added to the list of nutritional consequences while on the gluten-free diet and have been partially attributed to the hyper-caloric content of commercially available gluten-free foods.” (24)

Therefore, it is critical for people with Celiac Disease to learn how to eat a well balanced, nutrient-dense, fiber-rich diet while keeping the gluten-free substitutes to a minimum.

Based on the research discussed in this paper, I believe that it is also important to properly identify and correct nutrient deficiencies for each person with Celiac Disease.

In addition to conventional lab work, specialty labs such as SpectraCell and Vibrant America are providing new ways to assess nutrient status. For example, both labs offer intracellular micronutrient testing that allows clinicians to assess the functional status of nutrients within the cell vs. just what's found in the bloodstream.

Since increased intestinal permeability is thought to contribute to the development of food sensitivities it is also important to identify and remove other food antigens while comprehensively correcting increased intestinal permeability. (25)

In my opinion, this is best done through the combination of food sensitivity testing and by keeping a food journal to identify observable food reactions. Once the data from these two sources are obtained, people will have a better understanding of which foods to avoid and which foods to choose.

I believe it is also important to consider the gut microbiota when meal planning.

If dysbiosis is present, then it may be helpful for specific foods to be temporarily avoided and for other specific foods to be consumed along with the use of multi-strain probiotics, and even herbal antimicrobials when needed, to help support the rebalancing of the microbiome.

Once increased intestinal permeability has been resolved, and the gut microbiota is back in balance, healthy foods previously avoided (except for gluten) should be able to be reintroduced in an effort to find the least restrictive diet that supports the body’s continued ability to heal and function optimally. Lifelong avoidance of gluten is very important for those of us with Celiac Disease, but other foods not previously tolerated may be able to be successfully reintroduced if the proper steps have been taken.

In summary, the Functional Nutrition approach to supporting the health of someone with Celiac Disease includes:

1) transitioning to a healthy gluten-free life filled with a variety of nutrient dense whole foods personalized to the needs of each individual person

2) identifying and removing other food allergies or sensitivities

3) replacing the proper nutrients the body needs to function optimally

3) comprehensively addressing increased intestinal permeability and rebalancing the gut microbiota

4) implementing effective stress management techniques, emotional support and lifestyle changes that are supportive to the healing process

It is my hope that continued research will be done to identify additional nutritional interventions that can help with Celiac Disease.

To learn more about Celiac Disease and to find a local support group in your area, here are a couple helpful resources: The Celiac Disease Foundation and The Gluten Intolerance Group of America.


About Jaime

Jaime Ward, INHC, CGP, CBIN provides Functional & Integrative Nutrition Health Coaching for women and families living with Autoimmunity.

Jaime is Board Certified by the American Association of Drugless Practitioners, Certified in BioIndividual Nutrition, a Certified Gluten Practitioner, and currently pursuing a Master of Science degree in Clinical Nutrition with a focus on Functional Medicine from The University of Bridgeport.

Jaime is also a speaker, a writer, a busy mom, and a Celiac Disease Survivor. Jaime coaches with a Christian heart filled with lots of love, support and compassion.

For more information about how Jaime can help you, click here.



  1. Rubio-Tapia A, Ludvigsson JF, Brantner, et al. The prevalence of celiac disease in the United States. Am J Gastroenterol. 2012 Oct;107(10):1538-44; quiz 1537, 1545. Epub 2012 Jul 31.

  2. The University of Chicago Medicine: Celiac Disease Facts and Figures. Updated: Unknown. Accessed April 1, 2019.

  3. Barker JM, Liu E. Celiac disease: pathophysiology, clinical manifestations, and associated autoimmune conditions. Adv Pediatr. 2008;55:349-365.

  4. Cecilio LA, Bonatto MW. The prevalence of HLA DQ2 and DQ8 in patients with celiac disease, in family and in general population. Arq Bras Cir Dig. 2015;28(3):183-185.

  5. Kaukinen K, Partanen J, Maki M, Collin P. HLA-DQ typing in the diagnosis of celiac disease. Am J Gastroenterol. 2002 Mar;97(3):695-9.

  6. Celiac Disease Foundation: Celiac Disease Screening. Updated: Unknown. Accessed: April 1, 2019.

  7. Polvi A, Arranz E, Fernandez-Arquero M, et al. HLA-DQ2-negative celiac disease in Finland and Spain. Hum Immunol. 1998 Mar;59(3):169-75.

  8. Visser J, Rozing J, Sapone A, Lammers K, Fasano A. Tight junctions, intestinal permeability, and autoimmunity: celiac disease and type 1 diabetes paradigms. An N Y Acad Sci. 2009;1165:195-205.

  9. Cenit, MC, Olivares M, Codoner-Franch P, Sanz Y. Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution? Nutrients. 2015 Aug; 7(8): 6900-6923.

  10. Sarno M, Discepolo V, Troncone R, Auricchio R. Risk factors for celiac disease. Ital J Pediatr. 2015; 41:57.

  11. Kemppainen Km, Lynch KF, Liu E, et al. Factors That Increase Risk of Celiac Disease Autoimmunity After a Gastrointestinal Infection in Early Life. Clin Gastroenterol Hepatol. 2016;15(5):694-702.e5.

  12. Reisner E, Reisner, M. Crowley’s An Introduction to Human Disease: Pathology and Pathophysiology Correlations. 10th ed. Burlington, MA: Jones & Bartlett Learning; 2017.

  13. Kelly C, Bai J, Liu E, Leffler D. Advances in Diagnosis and Management of Celiac Disease. Gastroenterology. 2015 May;148(6):1175-1186.

  14. Celiac Disease Foundation: Diagnosis of Celiac Disease. Updated: Unknown. Accessed: April 1, 2019.

  15. McGowan K, Lyon M, Decker Butzner J. Celiac Disease and IgA Deficiency: Complications of Serological Testing Approaches Encountered in the Clinic. Clinical Chemistry. 2008;54(7):1203-1209.

  16. Pizzorno J, Katzinger J. Clinical Pathophysiology–A Functional Perspective: A Systems Approach to Understanding and Reversing Disease Processes. Coquitlam, BC Canada: Mind Publishing Inc.: 2012.

  17. Ojetti V, Gabrielli M, Migneco A, et al. Regression of lactose malabsorption in coeliac patients after receiving a gluten-free diet. Scand J Gastroenterol. 2008;43(2):174-7.

  18. Cukrowska B, Sowinska A, Bierla JB, et al. Intestinal epithelium, intraepithelial lymphocytes and the gut microbiota - Key players in the pathogenesis of celiac disease. World J Gastroenterol. 2017;23(42):7505-7518.

  19. Olivares M, Castillejo G, Varea V, Sanz Y. Double-blind, randomised, placebo-controlled intervention trial to evaluate the effects of Bifidobacterium longum CECT 7347 in children with newly diagnosed coelic disease. Br J Nutr. 2014 Jul 14;112(1):30-40.

  20. Francavilla R, Piccolo M, Francavilla A, et al. Clinical Microbiological Effect of a Multispecies Probiotic Supplementation in Celiac Patients with Persistent IBS-type Symptoms: A Randomized, Double-Blind, Placebo-controlled, Multicenter Trial. J Clin Gastroenterol. 2019;53(3):e117-e125.

  21. De Sousa Moraes LF, Grzeskowiak LM, de Sales Teixeira TF, Gouveia Peluzio Mdo C. Intestinal microbiota and probiotics in celiac disease. Clin Microbiol Rev. 2014;27(3):482-9.

  22. Cristofori F, Indrio F, Miniello VL, et al. Probiotics in Celiac Disease. Nutrients. 2018;10(12):1824. Published 2018 Nov 23.

  23. Smecuol E, Hwang HJ, Sugai E, et al. Exploratory, randomized, double-blind, placebo-controlled study on the effects of Bifidobacterium infantis natren life start strain super strain in active celiac disease. J Clin Gastroenterol. 2013 Feb;47(2):139-47.

  24. Theethira TG, Dennis M. Celiac disease and the gluten-free diet: consequences and recommendations for improvement. Dig Dis. 2015;33(2):175-82.

  25. Perrier C, Corthesy B. Gut permeability and food allergies. Clin Exp Allergy. 2011 Jan;41(1):20-8.

Featured Posts
Recent Posts
bottom of page