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A Functional Medicine Crohn's Disease Protocol: Specialty Testing, Nutrition, and Supplements

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A Functional Medicine Crohn's Disease Protocol: Specialty Testing, Nutrition, and Supplements

It is estimated that more than half a million people in the United States have Crohn's disease (CD), a type of inflammatory bowel disease (IBD). The incidence of Crohn's is rapidly increasing in the United States and industrializing areas of Asia, Africa, and Australasia. (1, 2)

CD can develop in people of any age but is more likely to develop in people between the ages of 20 and 29, who have a family member with IBD, and who smoke cigarettes. The disease runs a relapsing-remitting course and can progress from mild gastrointestinal inflammation to severe illness if chronic inflammation goes unmanaged. (1, 2)

Therefore, controlling inflammation and preventing disease relapse is critical in managing CD. A personalized functional medicine protocol discussed in this article targets key underlying causative factors, leading to improvements in disease prognosis and patient quality of life.


What is Crohn's Disease?

CD belongs to a group of conditions known as IBD, named after Dr. Burrill Crohn, who first described the disease in 1932. CD is characterized by intestinal inflammation affecting any portion of the gastrointestinal (GI) tract, from mouth to anus. However, it most commonly affects the end of the small intestine (ileum) and the beginning of the colon. The inflammation occurs in patches (called "skip lesions"), leaving unaffected areas between patches of diseased tissue extending through the entire thickness of the bowel wall. (3)

What Causes Crohn's Disease?

The causes of CD are not entirely understood; however, classified as an autoimmune disease, it is known that environmental triggers can stimulate an exaggerated immune response in genetically susceptible individuals, leading to chronic inflammation and the development of IBD.

Over one hundred genes are associated with IBD. Specific genes related to innate immune function and intestinal barrier integrity have been identified as contributors to the development and severity of CD. 8-12% of Crohn's patients have a family member with IBD. (4, 5)

Genetic susceptibility alone doesn't guarantee the development of IBD; environmental factors that have the power to turn on these genetic switches influence the likelihood of disease onset and progression. Western dietary patterns, smoking, infectious pathogens, intestinal permeability, and chronic use of non-steroidal anti-inflammatory drugs are known contributing factors to Crohn's autoimmunity. (4, 5)

Crohn's Disease Symptoms

CD most often begins gradually and worsens over time. Symptomatic flares occur between periods of remission, and each flare can cause increasing damage to the GI tract. Classic flare symptoms include (4-6):

  • Bloody diarrhea
  • Abdominal pain
  • Bloating
  • Nausea and vomiting
  • Mouth sores
  • Loss of appetite
  • Fever
  • Weight loss
  • Fatigue

Chronic inflammation also commonly presents with various extraintestinal symptoms, such as (4):

  • Eye pain, swelling, and inflammation
  • Joint pain and arthritis
  • Kidney stones and urinary tract infections
  • Skin rashes and lesions

Individuals with IBD have an increased risk for nutritional deficiencies due to the structural changes in the absorptive surface of the small intestine. Patients are most likely to develop iron, vitamin B12, vitamin D, folate, and vitamin K deficiencies. These deficiencies can cause their own sets of symptoms, like fatigue, depression, poor wound healing, easy bleeding, and brittle hair/nails. (5)

CD is associated with an elevated risk of health complications, which include (4, 5):

How Is Crohn's Disease Diagnosed?

A Crohn's disease diagnosis requires the integration of medical history, physical exam, laboratory tests, endoscopy and radiographic results, and GI pathology findings. CD should be suspected in patients with cardinal clinical symptoms (chronic diarrhea and abdominal pain) and laboratory signs of inflammation (elevated ESR, CRP, and calprotectin). (7)

Colonoscopy is recommended as part of the initial evaluation of patients with suspected IBD; over 80% of patients with IBD will have mucosal involvement within reach of the colonoscope. Upper endoscopy should also be recommended for those with upper GI signs and symptoms. Endoscopic features of CD include discontinuous transmural asymmetric inflammation, longitudinal and serpiginous ulcerations and fissures, and cobblestone appearance. Histopathologic features that confirm CD diagnosis include granulomatous inflammation, transmural inflammation, and fissures or aphthous ulcers. (7)

Functional Medicine Labs to Test for Root Cause of Crohn's Disease

After a patient has been diagnosed with CD, functional medicine tests can help provide insight into the underlying factors contributing to disease pathogenesis and severity.

Celiac, IBS, and Crohn's Assay

The Celiac, IBS, and Crohn's Assay (CICA) evaluates genetic and serological markers for celiac and Crohn's disease. While serum testing is not gold-standard for a definitive diagnosis of celiac or Crohn's disease, positive findings increase the likelihood of either diagnosis. Evidence suggests that celiac disease significantly increases the risk of developing IBD (4). This panel also includes the anti-Saccharomyces cerevisiae antibody (ASCA), which may be produced by the immune system against a specific type of yeast and indicates CD's presence and severity.

Comprehensive Gut Assessment

A combination of stool, breath, and serum tests can thoroughly evaluate intestinal integrity, digestive function, and the makeup of the intestinal microbiome.

A comprehensive stool analysis is an all-encompassing test that includes fecal inflammatory, digestive, and microbial markers that can quantify the severity of IBD and assess dysbiotic patterns that can contribute to inflammation, autoimmunity, and intestinal permeability.

Small intestinal bacterial overgrowth (SIBO) occurs when bacteria overpopulate the small intestine. SIBO can exacerbate GI symptoms, intestinal permeability, autoimmunity, and systemic inflammation. Studies demonstrate increased rates of SIBO in patients with IBD and reductions in IBD symptoms by eradicating bacteria from the small intestine (6). SIBO can be diagnosed by endoscopy or an at-home breath test.

A leaky gut panel measures serum antibodies to actin, zonulin, and lipopolysaccharides to diagnose the presence and mechanism behind leaky gut/intestinal permeability.

Functional Medicine Labs That Can Help Individualize Treatment for Crohn's Disease Patients

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for Crohn's patients.

Inflammatory Markers

Fecal and serum inflammatory markers are non-invasive and cost-effective alternatives to endoscopic imaging to monitor IBD. The most common inflammatory markers ordered in clinical practice include serum CRP, fecal calprotectin, and fecal lactoferrin.

Food Sensitivities

Incorporating food sensitivities into the diet can contribute to Crohn's symptoms and perpetuate chronic intestinal inflammation. Therefore, identifying food sensitivities may be an important aspect of the treatment plan to personalize a therapeutic elimination diet that provides an opportunity for gut rest and repair.

Nutritional Assessment

Suboptimal and frankly deficient nutrient status caused by impaired intestinal absorption leads to extraintestinal symptoms, impair intestinal healing, and increases the risk for secondary health complications (i.e., osteoporosis). Ordering a micronutrient panel aids in the nutritional status of patients so that dietary and supplemental interventions can be tailored to the patient's nutritional needs.


Conventional Treatment for Crohn's Disease

Pharmacologic therapies for patients with CD include corticosteroids, immunomodulators, and biologic agents to induce and maintain disease remission. Treatment decisions are guided by age, comorbidities, symptoms, inflammation status, disease location and extent, and overall risk of more severe and complicated disease. (8)

Functional Medicine Treatment Protocol for Crohn's Disease

The safety profile, decreased expense, efficacy, and root cause approach of functional medicine treatment options make them worthwhile considerations. It should be noted that conventional pharmacotherapy may still be required in some instances to prevent serious health complications and the need for gastrointestinal surgical interventions. However, many times, incorporating natural therapeutics that address the underlying cause of CD pathology reduces disease severity, prevents health complications, and lessens the need for pharmacologic interventions.

Therapeutic Diet and Nutrition Considerations for Crohn's Disease

Therapeutic goals of nutritional therapy for patients with CD include meeting adequate caloric and nutrient needs from their diets and making dietary modifications to reduce inflammation (9).

Diets that contain pro-inflammatory foods, such as the Standard American Diet (SAD), are risk factors for the development of CD and nutrient deficiencies. Researchers suggest that individuals with CD should focus on anti-inflammatory diet protocols, including the Mediterranean, low-FODMAP, Paleo, and specific carbohydrate diets. These diets emphasize avoiding foods that trigger inflammatory responses while incorporating colorful fruits, non-starchy vegetables, and anti-inflammatory spices. (9, 10)

The elemental diet is a well-researched therapeutic nutritional intervention for Crohn's disease. This predigested, hypoallergenic formula is a complete meal replacement that meets nutritional and caloric needs while providing respite for the gut during Crohn's flares. Research strongly supports the use of the elemental diet to induce disease remission, prevent CD relapse, and improve the nutritional status of patients. The elemental diet can be initiated at the first sign of a symptom flare. The powdered formula is mixed in water and drunk throughout the day for 2-4 days. Nothing other than the elemental formula and water should be consumed during an elemental diet. (11-13)

Supplements Protocol for Crohn's Disease

Dietary and herbal supplements are used to supplement dietary and lifestyle interventions to support the nutritional status of patients, reduce inflammation, and assist gut healing.


A high-potency, broad-spectrum multivitamin may be beneficial to recommend to patients with a high risk of nutrient deficiencies to support nutritional needs and correct identified deficiencies on lab testing.

Dose per label instructions

Duration: as needed


This herbal and proteolytic enzyme formula by Vital Nutrients supports a healthy inflammatory response in the digestive tract and joints. This formula combines Boswellia, curcumin, quercetin, and bromelain. These ingredients exert anti-inflammatory and analgesic effects by inhibiting inflammatory biochemical pathways and modulating substance P, a neuropeptide that modulates pain perception. (14)

Dose: 3 capsules 2-4 times daily in between meals

Duration: at least three months


Resveratrol is a naturally occurring polyphenol with anti-inflammatory, anticancer, and antioxidant properties. In the last decade, increasing attention has been placed on its clinical application in treating chronic disease. Resveratrol has several key features that make it particularly qualified for managing CD, which include its ability to improve intestinal barrier function, regulate an unbalance gut microbiota, downregulate inflammatory signaling pathways, and protect against uveitis. (15, 16)  

Dose: 50 mg twice daily

Duration: at least six weeks


L-glutamine is an amino acid used as the primary fuel source by the cells lining the small intestine. Glutamine metabolism, and thus demand, is increased during active intestinal inflammation. In fact, glutamine colonic tissue levels of patients with IBD are decreased compared to healthy controls. Oral or rectal glutamine supplementation attenuates intestinal inflammation and fibrosis, improves histology results, reduces oxidative stress and inflammatory cytokines, and preserves gut barrier function. (18)

Dose: 5 grams twice daily

Duration: 12 weeks

Vitamin D

Vitamin D deficiency is common in IBD, may contribute to disease development, and is associated with increased disease severity. Vitamin D supplementation can correct and optimize serum vitamin D status, resulting in immune regulation, reduced inflammation, and reduced risk of cancer, anemia, and osteoporosis. (4, 17)

Dose: 2,000-10,000 IU daily; dose should be determined by the patient's serum vitamin D status

Duration: 6-12 months


Probiotics are live microorganisms that improve the gut flora and confer health benefits to the host when administered in therapeutic doses. Dysbiosis is associated with immune dysregulation, intestinal permeability, inflammation, and autoimmunity. Probiotics can restore the microbiome to a healthy state. (10)

RestorFlora™ combines three well-studied probiotic strains - Saccharomyces boulardii, Bacillus subtilis, and Bacillus clausii. Research demonstrates that each of these probiotics can promote a healthy intestinal environment by regulating inflammation, improving intestinal integrity, and treating GI symptoms.

Dose: one capsule daily

Duration: 1.5-6 months

When to Retest Labs

Patients should expect to begin to see results with the treatment protocol within a couple of weeks of initiation. It may take up to three months for a natural treatment plan to have full effect, so while labs could be retested as soon as one month, it may be worthwhile to postpone reevaluation. Patients with more severe disease should be more closely monitored for health complications and side effects of pharmacologic agents.



Crohn's disease is a form of inflammatory bowel disease that can cause irreversible gastrointestinal damage and related health complications if not managed appropriately. Conventional interventions focus on using medications to control dysfunctional immune responses and inflammation. While this may be effective in initiating remission, they are often accompanied by undesirable cost and side effect profiles. As outlined in this article, a functional medicine protocol is an alternative option to address the root causes of gastrointestinal inflammation, prevent health complications, and improve prognostic outcomes.

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

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13. Teahon, K., Bjarnason, I., Pearson, M., et al. (1990). Ten years' experience with an elemental diet in the management of Crohn's disease. Gut, 31(10), 1133–1137.

14. Moehle, J., Fuller, L., & Hardin, A. (2021). Fish Oil and BCQTM as a Novel Treatment Approach to Primary Erythromelalgia: A Case Study. Integrative Medicine (Encinitas, Calif.), 20(4), 40–45.

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18. Sugihara, K., Morhardt, T. L., & Kamada, N. (2019). The Role of Dietary Nutrients in Inflammatory Bowel Disease. Frontiers in Immunology, 9.

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