7 min|Dr. Maya Kuczma

Autoimmune Disease 101: Treatment of Celiac Disease

Gut Health, Autoimmune Disease

In Part One of this series, we discussed the signs and symptoms of celiac disease, how it develops, how to test for it, and who should be tested.

Below, we will focus on the necessary steps following diagnosis, including treatment, both conventional and alternative, as well as management.

What is the treatment for celiac disease?

The most important treatment component for patients with celiac disease is a complete, lifelong avoidance of gluten and all gluten-containing grains and products. Eating any gluten, regardless of whether it triggers immediate symptoms or not, damages the small intestine in those with celiac disease. Complete avoidance of gluten can slowly stop the process of intestinal damage; however, certain symptoms associated with celiac disease, such as dental enamel defects or delayed growth may not improve, depending on the severity of the disease process and length of time before diagnosis. Additionally, even on a gluten-free diet, antibodies can remain elevated for up to two years, indicating that villous damage characteristic of celiac disease can continue for a length of time following removal of gluten; this timeline is likely exacerbated with each exposure to gluten.(1)

A gluten-free diet requires complete avoidance of all gluten-containing grains, such as wheat, spelt, rye, and barley. Obvious sources of these grains include breads, pastas, pizza, pastries, crackers, and cookies. However, there are many, many other less obvious sources of gluten, such as certain sauces, marinades, salad dressings, gravy, candy, chocolate bars, chips, gums, supplements, and medications.

Complete avoidance of gluten requires a masterful eye, and becoming very familiar with ingredient labels. Even if something ‘looks like it doesn’t have gluten’ - check the label. Best laid plans can be foiled by a sneaky addition of gluten to packaged foods. Your safest bets, barring any additional food sensitivities and/or allergies, are whole, unprocessed foods, such as meat, chicken, fish, eggs, veggies, fruits, nuts, and seeds.


Another dietary consideration for people living with celiac disease is cross-contamination. This refers to the process of inadvertent contamination with gluten, and is most likely to happen at restaurants where they do not have a separate preparation area, oven, and/or deep fryer for gluten-free items. There is a possibility that a gluten-free item, such as a gluten-free pizza, prepared or cooked in an area near gluten-containing items, will become contaminated with gluten, and could trigger an inflammatory reaction if ingested by someone with Celiac disease.

In a study of Celiac patients, 91% experienced symptoms while following a gluten-free diet due to accidental exposure; these exposures mostly occurred at restaurants or when dining at friend’s homes. (2) This can make dining-out, or dining at friends' homes difficult to navigate. However, increasingly, restaurant staff appear to be well-versed in celiac disease and understand the seriousness of contamination, while others maintain a completely gluten-free kitchen. We recommend discussing your concerns with the restaurant manager or host prior to dining out to create a positive dining experience.

Gut Healing

All of the treatments we’ve discussed so far focus on eliminating the trigger of celiac disease: gluten. Complete gluten avoidance is challenging, and even with complete avoidance, many patients with celiac disease notice improvements slowly, over months or even years. Additionally, subjective improvements are not always a reliable indicator of gut mucosal recovery. (3) For these reasons, a completely gluten-free diet is necessary, but often not a sufficient treatment plan for those of us with celiac disease. Ideally, further steps are taken to support and accelerate gut healing.

Although celiac disease is thought to be largely dictated by genetics, studies have shown that up to 55% of the population that carries at least a single copy of the gene associated with celiac do not go on to develop celiac disease. (4) This indicates that although genetic predisposition and gluten exposure are required for the development of celiac disease, these two factors alone are insufficient in many cases. There is a growing body of research indicating that imbalances within the gut microbiome may play a key role in ‘activating’ the genes associated with celiac disease, turning gluten into a potent trigger of gut inflammation and damage. (5) 

While the specifics of this pathophysiology - and how to correct it - are still not fully understood, investigation of the microbiome of patients with celiac disease, via a complex stool analysis and SIBO breath testing, is warranted, and can help guide our treatment of microbiome imbalances. This can lead to treatment of pathogenic viruses, yeasts, parasites, and/or bacteria, as well as individualized reinoculation with healthy probiotic species.

Specific supplements can also be utilized to restore integrity of the intestinal barrier, decrease inflammation within the gut lining, and replace nutrients commonly depleted as a result of celiac disease, such as iron, B12, and folate. For example, depletion of glutamine, an amino acid, leads to villous atrophy and increased intestinal permeability; (6) supplementation with glutamine can improve the integrity of the gut barrier.

Additionally, replacement of digestive enzymes can be helpful, as celiac disease is associated with a decreased ability to produce digestive enzymes, known as exocrine pancreatic insufficiency. (7) Supplementation of DPP-IV, an enzyme that plays a role in gluten degradation, may be helpful in decreasing the inflammatory effects of small amounts of gluten, such as during cross-contamination; however, current research does not indicate that DPP-IV can negate the effects of a gluten-containing diet. (8) Typically, a comprehensive digestive enzyme, including DPP-IV, is a helpful addition to the main treatment - a gluten-free diet.


Currently, many medications for celiac disease are in development; these medications aim to interrupt the immune response to gluten, induce immune tolerance, or increase enzymatic breakdown of gluten. (9) Time will tell whether these medications are effective and safe.

For now, the most interesting consideration regarding medication is the association between certain medications and persistent villous atrophy - the significant damage within the small intestinal lining that is characteristic of celiac disease. Certain medications, such as acid reducing medications (also known as PPIs), a class of antidepressants (SSRIs), and non-steroidal anti-inflammatories (NSAIDS), have all been associated with persistent villous atrophy in celiac patients who are already on a gluten-free diet. (10) For patients with celiac disease, it may be pertinent to determine alternatives to these medications, whenever possible, that do not carry this adverse effect.

On-Going Management

Specific tests can be completed to determine the systemic effects of celiac disease, and re-tested to monitor response to a treatment plan:
  • Anemia profile (hemoglobin, hematocrit, folate, ferritin, B12)
  • Complete blood count
  • Vitamin D
  • Lipid profile
  • Electrolyte and kidney profile
  • Liver profile
  • Full Thyroid Panel, including antibodies
  • Additional autoimmune markers, such as ANA, Rh
  • Bone density scan
Additionally, repeat testing of Celiac associated antibodies can be helpful in monitoring response to a gluten-free diet:
  • Blood Test - Tissue Transglutaminase Antibodies:
    • Anti-TTG IgA
    • Anti-TTG IgG: a helpful additional test in patients with suspected IgA deficiency
  • Blood Test - Deamidated Gliadin Antibodies: should be included when testing children and those with IgA deficiency
    • Anti-DGP IgA
    • Anti-DGP IgG
Lastly, working one-on-one with a Naturopathic Doctor can help monitor your symptoms and progress. They can develop an individualized treatment plan that goes beyond gluten elimination to support gut healing, balance the microbiome, reduce your symptoms, and lessen your risk of developing further autoimmune conditions.

Do you have signs or symptoms associated with Celiac disease? Have you already eliminated gluten, and are wondering if there’s more you could be doing to support your body or to further investigate celiac disease?

At Integrative, we’re here to help. Book your one-on-one initial consultation today.

  1. https://onlinelibrary.wiley.com/doi/full/10.1111/apt.15277
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283559/
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881171/
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737358/
  5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835875/
  6. https://pubmed.ncbi.nlm.nih.gov/27749689/
  7. https://link.springer.com/article/10.1007/s10620-010-1261-y
  8. https://www.frontiersin.org/articles/10.3389/fped.2019.00193/full
  9. https://www.beyondceliac.org/research/drugdevelopment/drug-development-pipeline/
  10. https://celiacdiseasecenter.columbia.edu/wp-content/uploads/2018/12/Factors-associated-with-villus-atrophy-in-symptomatic-coeliac-disease-patients-on-a-gluten-free-diet.pdf
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