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A Functional Medicine Celiac Disease Protocol: Specialty Testing, Nutrition, and Supplements

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A Functional Medicine Celiac Disease Protocol: Specialty Testing, Nutrition, and Supplements

Celiac disease, or gluten-sensitive enteropathy, is a genetic autoimmune disease that damages the small intestine's villi, causing intestinal damage and chronic malabsorption of essential nutrients. An estimated 1% of Americans and 1.4% of the global population have celiac disease. However, more recent studies estimate that the incidence of celiac disease, especially in the pediatric population, has increased by 7.5% per year over the recent decades. (1-4)

Because a gluten-free diet is the only existing treatment for celiac disease, early diagnosis and dietary modification are required to prevent irreversible intestinal damage and health complications. Unfortunately, this is not always the case. An estimated 83% of Americans with celiac disease go un- or misdiagnosed, and it takes on average 6-10 years and nearly $4,000 in healthcare costs to receive the correct diagnosis. (2)

This article will discuss a functional medicine protocol that can be implemented in clinical practice to diagnose and treat celiac disease.


What is Celiac Disease?

Celiac disease (CD) is a chronic, inflammatory condition in which the body produces an autoimmune reaction in response to exposure to gluten, a protein found in grains like wheat, barley, rye, and spelt. Autoantibodies produced in this immune response target and cause damage to small intestinal villi, finger-like projections that play a crucial role in nutrient absorption.

CD is clinically distinct from non-celiac gluten sensitivity (NCGS) and wheat allergy, neither of which are autoimmune in nature but may present with similar digestive symptoms.

Celiac Disease Symptoms

Classic digestive symptoms of CD include (7):

  • Diarrhea and/or constipation
  • Gas and bloating
  • Abdominal pain
  • Nausea and vomiting

Malabsorptive Disorder Symptoms

Extraintestinal manifestations of the disease are also common, caused by nutrient malabsorption. Signs and symptoms of malabsorptive disorders include (1, 5):

  • Fatigue
  • Failure to thrive (in children) and weight loss (in adults)
  • Recurrent canker sores (aphthous ulcers)
  • Iron deficiency anemia (IDA)
  • Chronic headaches
  • Delayed puberty

Celiac Disease Autoimmune Comorbidities

Untreated and undiagnosed CD is associated with an increased risk of developing other autoimmune disorders, like type 1 diabetes and multiple sclerosis, and other conditions, including (6):

What Causes Celiac Disease?

Researchers have identified genetic and environmental factors that contribute to the development of celiac disease. Genetic predisposition to the disorder occurs when an individual carries the HLA DQ2 and/or DQ8 gene. Individuals with a parent, sibling, or child with CD are ten times more likely to develop the condition. (1, 5)

CD is also more common in people with type 1 diabetes, Down syndrome, Turner syndrome, autoimmune thyroid disease, microscopic colitis, and Addison’s disease (7).

Despite the important genetic component of disease development, not all HLA carriers will develop an autoimmune response to gluten. This indicates environmental factors significantly impact the initiation of gluten autoimmunity in genetically susceptible individuals. Gastrointestinal infection during early childhood and intestinal dysbiosis, possibly influenced by Cesarian delivery and formula feeding, have all been implicated in increasing the risk of CD (1, 8).

Functional Medicine Labs to Test for Root Cause of Celiac Disease

Gold-standard diagnosis of CD requires a small intestinal endoscopy with duodenal biopsy that confirms histological small intestinal villous atrophy specific to CD. Given this procedure's cost and invasive nature, however, serological testing is typically ordered first to differentiate celiac disease from other gastrointestinal conditions and gauge the need to order endoscopic imaging. (9)

Celiac Panel

Current diagnostic guidelines recommend measuring serum tissue transglutaminase (tTG) IgA antibodies in patients consuming gluten daily for 6-8 weeks as a first-line screening for CD (9). Specialty celiac and gluten sensitivity panels typically include total IgA; IgA and IgG antibodies to tTG, endomysial, and deamidated gliadin peptide; and HLA DQ2 and DQ8 to increase testing accuracy.

Comprehensive Stool Test

Intestinal dysbiosis and reduced microfloral biodiversity, specifically reductions in beneficial Lactobacillus and Bifidobacterium species and increases in potentially pathogenic Bacteroides and E. coli, are noted in patients with CD. A comprehensive stool test assesses the gut microbiome, measures intestinal inflammation, and screens for malabsorption to provide insight into the cause of gluten autoimmunity and guide treatment to correct intestinal imbalances.

Functional Medicine Labs That Help Individualize Treatment for Celiac Disease Patients

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for patients suffering from celiac disease.

Thyroid Panel

Patients with CD have a four times higher prevalence of autoimmune thyroid disease than the general population. A complete thyroid panel that measures TSH, thyroid hormones, and thyroid antibodies should be ordered to screen for thyroid autoimmunity and thyroid disease.

Food Sensitivities

Inflammation and leaky gut caused by autoimmune-induced small intestinal damage increase the risk of other food sensitivities, further perpetuating intestinal inflammation and diminishing the healing response. A food sensitivity panel can help identify food sensitivities so that a short-term elimination diet can be initiated in addition to a gluten-free diet to speed intestinal recovery.

Additionally, certain dietary proteins can cross-react with gluten. Cross-reactivity occurs when food proteins appear similar to gluten and trigger the celiac autoimmunity response. For patients not improving on a gluten-free diet, a gluten cross-reactivity panel can identify other foods they are intolerant to and may need to eliminate from the diet.

Micronutrient Testing

Micronutrient deficiencies, in particular iron, folic acid, vitamins B6 and B12, vitamin D, copper, and zinc, are common in celiac patients. A micronutrient panel measures nutrient status at a cellular level to identify nutrient imbalances contributing to anemia, neurological complications, psychiatric symptoms, and reduced bone density in patients with CD.


Functional Medicine Treatment Protocol for Celiac Disease

Successfully treating celiac disease requires a multimodal approach that includes strict gluten avoidance and acknowledging underlying factors leading to autoimmunity. A functional medicine treatment protocol prevents future autoimmune reactions and supports small intestinal healing.

Therapeutic Diet and Nutrition Considerations for Celiac Disease

Strict life-long gluten elimination is the only treatment for CD. The gluten-free (GF) diet completely eliminates all gluten-containing foods and beverages. It is also imperative to avoid gluten cross-contamination, which occurs when gluten-free foods are prepared or manufactured on common surfaces with gluten-containing foods. When buying packaged foods, patients should look for the "Certified Gluten-Free" label to ensure food safety. It should also be noted that "wheat free" is not the same as "gluten-free."

Most patients find almost immediate relief from symptoms after initiating a GF diet. Patients not responding as expected may be experiencing cross-reactivity or other food sensitivity reactions. In these cases, further testing and therapeutic dietary eliminations may be required. Identified or suspected food sensitivities should be eliminated from the diet for at least 4-6 weeks until patient symptoms resolve. The patient can then be instructed to reintroduce foods back into the diet individually over three days. On the first day of the reintroduction challenge, the patient should eat one serving of the chosen food three times throughout the day. Days two and three are meant for observation; the food will not be consumed during this time. At the end of the third day, if the patient has not experienced any adverse reactions, they can reincorporate the food into the diet. Any foods that elicit symptoms should continue to be avoided in the diet.

Supplements Protocol for Celiac Disease Patients

While adherence to a GF diet is non-negotiable for healing the small intestinal mucosa, natural supplementation may be necessary to expedite healing, reduce inflammation, and correct nutritional deficiencies. Evidence-based supplements to consider recommending to patients with CD are summarized below.


EnteroMend® is Thorne's botanical and amino acid formula combining L-glutamine, curcumin, Boswellia, aloe vera, and partially hydrolyzed guar gum (PHGG). Anti-inflammatory herbs curcumin, Boswellia, and aloe maintain healthy levels of inflammation within the bowel and support normal gastrointestinal function. L-glutamine is the preferred fuel source of cells lining the small intestine and reduces intestinal permeability. PHGG is a fiber that feeds the colonic microflora and helps regulate bowel function and the intestinal microbiota. Butyrate, a short-chain fatty acid, is derived by microbial fermentation of PHGG and acts to regulate immune function.  

Dose: two scoops mixed in water twice daily

Duration: 1-3 months


Because comparisons between people with and without CD show distinct differences in microbiota profiles, it is speculated that dysbiosis is involved in CD pathology. Bacterial species belonging to the genera Lactobacillus and Bifidobacterium exert protective properties on epithelial cells and support the digestion of gluten proteins. (10)

VSL#3® is a high-dose, medical-grade probiotic that contains eight bacterial strains and is backed by evidence to regulate intestinal barrier function by improving tight junction function, balancing microbial composition, and regulating immune-related cytokine expression (11). Research also demonstrates this probiotic's capacity to digest gluten proteins responsible for CD.

Dose: 1-2 capsules daily

Duration: 12 weeks


A high-potency multivitamin and mineral supplement may be necessary in cases where nutritional deficiencies persist despite adherence to a GF diet. A daily multivitamin can address general nutrient deficiencies and prevent symptoms and health conditions related to nutrient imbalances.

Dose: Per label instructions

Duration: Ongoing until nutrient deficiencies have been corrected and nutrient status is sustained by diet alone


Emerging research suggests that gluten-specific enzymes and probiotics can support gluten degradation in the stomach before they pass into the small intestine. WheatRescue™ by Microbiome Labs is a digestive formula containing probiotic spores and digestive enzymes to support gluten digestion. It is important to note that digestive enzymes cannot replace strict gluten elimination but can be used as a rescue remedy in cases of accidental gluten exposure to reduce negative side effects.

Dose: 1 capsule with meal

Duration: as needed for accidental gluten exposure

When to Retest Labs

Most people experience symptom improvement almost immediately after starting a GF diet, but it may take several weeks to months to correct nutritional deficiencies and heal the gut entirely. Any baseline deficiencies and lab abnormalities can be monitored 4-6 weeks after the initiation of supplementation to assess patient response to therapy and adjust dosing as needed. Celiac antibodies can also be remeasured 1-3 months after starting a GF diet. Although achieving a negative antibody panel may take 6-12 months, a steady reduction of celiac antibodies should be noted. Patients without normalizing celiac panels are likely exposed to hidden sources of gluten, which should be identified and removed.



Celiac disease is a small intestinal autoimmune reaction to gluten exposure in genetically susceptible individuals that can be difficult to diagnose given its variable clinical presentations. However, early detection and treatment are essential to prevent serious chronic health complications and improve patient quality of life. Functional medicine offers a holistic and comprehensive approach to testing and treatment that can expedite accurate diagnosis, reduce intestinal inflammation, and heal small intestinal damage.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. Posner, E. B., & Haseeb, M. (2020). Celiac Disease. PubMed; StatPearls Publishing.

2. Beyond Celiac. (2010). Celiac Disease: Fast Facts. Beyond Celiac.

3. ​​Singh, P., Arora, A., Strand, T.A., et al. (2018). Global Prevalence of Celiac Disease: Systematic Review and Meta-analysis. Clinical Gastroenterology and Hepatology, 16(6), 823-836.e2.

4. King, J.A., Jeong, J., Underwood, F.E., et al. (2020). Incidence of Celiac Disease Is Increasing Over Time. The American Journal of Gastroenterology, 115(4), 1.

5. Robinson, K. (2020, October 8). Understanding Celiac Disease: Symptoms, Health Risks, and Treatment. Fullscript.

6. Celiac Disease Foundation. (2017, December 31). What Is Celiac Disease? Celiac Disease Foundation.

7. Mayo Clinic. (2021, August 10). Celiac Disease - Symptoms and Causes. Mayo Clinic.

8. Cesarean section, antibiotics and formula cause changes in the immune system of babies at risk for celiac disease. (2020, September 30). Beyond Celiac.

9. Pelkowski, T.D., & Viera, A.J. (2014). Celiac Disease: Diagnosis and Management. American Family Physician, 89(2), 99–105.

10. de Sousa Moraes, L.F., Grzeskowiak, L.M., de Sales Teixeira, T.F., et al. (2014). Intestinal Microbiota and Probiotics in Celiac Disease. Clinical Microbiology Reviews, 27(3), 482–489.

11. Cheng, F.S., Pan, D., Chang, B., et al. (2020). Probiotic mixture VSL#3: An overview of basic and clinical studies in chronic diseases. World Journal of Clinical Cases, 8(8), 1361–1384.

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