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Crohn’s and Gluten: Why Elimination Diets Might Not Be Enough

Updated on January 3, 2023

  • Gluten can have a detrimental impact on patients with Crohn’s disease, regardless of whether or not they have a discrete gluten intolerance.
  • A number of gluten-free diets can help patients eliminate gluten, but evidence for their therapeutic efficacy is inconsistent.
  • Nutritional supports designed to enhance gut microbiome health, such as butyric acid supplements, can work in concert with gluten-free diets or be used on their own to support effective and durable symptom relief.

Although gluten intolerance is traditionally associated with celiac disease, this understanding is shifting as the medical community increasingly recognizes both non-celiac gluten sensitivity and the impact of gluten on other health conditions. In particular, the relationship between Crohn’s and gluten has become a critical area of interest, spurring many patients to consider gluten-free diets (GFDs) as potentially effective therapies. By exploring the current literature, clinicians and patients can come to understand both the potential and limits of gluten elimination and why additional dietary support in the form of supplementation might be necessary to obtain symptom management.

Crohn’s and Gluten: The Impact on Patients

Despite the close relationship between celiac disease and gluten intolerance, gluten sensitivity is experienced by individuals without celiac disease. As Chris Kresser, director of the California Center For Functional Medicine, states, “It’s becoming more and more clear that celiac disease is only one manifestation of gluten intolerance, and that ‘non-celiac gluten sensitivity’ (i.e., people who react to gluten but do not have celiac disease) is a legitimate health condition.” As Kresser notes, gluten sensitivity is newly recognized as a pathology in its own right rather than as a symptom of other underlying pathologies, like it is in celiac disease, and such sensitivity can aggravate symptoms of co-occurring Crohn’s disease. Additionally, patients with Crohn’s can be susceptible to gluten-induced gastrointestinal distress due to the impact of gluten on the gut microbiome. In light of the relationship between Crohn’s and gluten, the rationale for using a gluten-free diet is twofold:

Gluten Sensitivity In Crohn’s Patients

Crohn’s disease patients can have gluten intolerance that is separate from their Crohn’s pathology but augments Crohn’s symptoms when triggered. This occurs when B-cells of the immune system are activated by gluten consumption and consistently and incorrectly produce antibodies against it, inducing a minor allergic reaction and subsequent inflammation. While this can occur in non-Crohn’s patients, those with Crohn’s are particularly vulnerable to such a reaction due to abnormally active immune cells in the GI tract, which occurs independently of specific allergens. As a result, Crohn’s patients produce antibodies against many common but harmless antigens present in food, leading to heightened risk of immune activation and inflammation while stopping short of a major allergic reaction. Although wheat gluten antigens are just one set of many other antigens that can trigger Crohn’s disease patients into a flare-up, gluten is a particularly common culprit; one study found that 29.3 percent of Crohn’s patients experience non-celiac gluten sensitivity.

The Effect of Gluten on the Microbiome

In addition to the inflammation caused by allergic reaction, gluten can cause inflammation of the GI tract by inducing dysbiosis, thereby destabilizing the gut microbiome’s bacterial proportions. Dysbiosis means the immune system is allowing or causing harmful bacteria to out-compete the beneficial bacteria that are characteristic of a healthy microbiome. Once the microbiome is disrupted by an abundance of easy-to-consume fuel in the form of wheat gluten proteins, unhealthy bacteria can rapidly replicate themselves and displace normal microbiomic fauna, causing the immune system to generate more inflammation. Inflammation and de-inflammation cycles can then cause micro-tearing of the intestinal surfaces, causing bleeding and bloody stools.

Additionally, Crohn’s patients often require microbiome-disrupting therapies like antibiotics to control their symptoms. As Kresser notes, “Just a single course of antibiotics can reduce the richness and diversity of the intestinal microbiota, and in many cases, an individual can never completely regain the diversity they lost.” Considering the potential detrimental effects that gluten can have on the microbiome and the generally disrupted state of the microbiome in Crohn’s patients, minimizing gluten consumption might thus make the difference between a destabilized and a balanced microbiome.

Gluten-Free Diets for Crohn’s

Given the link between gluten and Crohn’s symptoms, a growing body of research is highlighting the potential advantages of gluten elimination. One particularly promising investigation found that 65.6 percent of Crohn’s patients experienced better management of one or more of their symptoms while on a GFD. 23.6 percent of these patients used fewer medications to address flare-ups, and 38.3 percent of these patients reported fewer flare-ups overall. This data suggests that a GFD can have a meaningful impact on many Crohn’s patients.

Although the study did not inquire about the specific GFD used by participants, several GFDs have been investigated for their efficacy in addressing Crohn’s disease and other IBDs:


The most heavily-researched GFD used by Crohn’s patients is the specific carbohydrate diet (SCD). Originally intended to address the symptoms of celiac disease before celiac disease itself was characterized, the SCD’s goal is to control the gut microbiome by regulating carbohydrates that are easily broken down by bacteria. In practice, this means eliminating the majority of carbohydrates altogether, with a particular emphasis on removing carbohydrates that produce gas when digested, including all grains. As a result, SCD is incidentally gluten-free.

A study investigating the efficacy of different diets in the context of Crohn’s disease and ulcerative colitis found that the SCD benefitted both sets of patients. The study found that 42 percent of Crohn’s disease and ulcerative colitis patients experienced less inflammation and gastrointestinal disturbances after six months of the SCD. Of this 42 percent, 13 percent reported that remission began within two weeks of starting the SCD. However, the SCD isn’t sufficient to slow down flaring Crohn’s symptoms; once an inflammatory chain reaction begins, it’s too late to switch to a different diet. Additionally, the SCD was not designed with a modern understanding of microbiome health or Crohn’s disease. As such, it is not an optimal strategy for Crohn’s patients, despite being helpful for some.


Originally developed by Drs. Stein and Baldrassano of the Children’s Hospital of Pennsylvania, the Crohn’s Disease Exclusion Diet (CDED) is a new GFD designed specifically to promote microbiome health and to address the symptoms of Crohn’s patients. By excluding those foods to which Crohn’s patients are most likely to experience sensitivity—gluten, milk, beef, pork, and eggs—the diet seeks to address the runaway inflammation that damages the microbiome. As an emerging therapy, the CDED remains under investigation. 

FODMAP Exclusion Diets

The FODMAP (Fermentable Oligo-/Di-/Mono-saccharides And Polyols) exclusion diets are designed to address a wide variety of gastrointestinal disorders, ranging from irritable bowel syndrome (IBS) to inflammatory bowel syndromes like Crohn’s, by reducing the intake of foods that produce large volumes of gas when fermented in the intestinal tract. FODMAP diets are often incidentally gluten-free, although their main focus is the exclusion of certain carbohydrates, referred to as FODMAPs, that are poorly absorbed by the GI tract.

The evidence for FODMAP diets in Crohn’s disease is conflicting. A number of studies have found that FODMAP exclusion diets are linked to reduced GI inflammation and other symptoms in inflammatory bowel diseases. Other studies, however, have not replicated these results. Furthermore, FODMAP diets can lower butyrate production and cause maladaptive changes in the microbiome, which could potentially aggravate GI inflammation. Future research needs to clarify the conflict and determine whether FODMAP diets are useful.

A Possible Explanation for Inconsistent Findings

Although diets can provide relief to some patients, the inconsistent evidence finding on the efficacy of GFDs for Crohn’s patients might have an explanation. The group of human leukocyte antigen (HLA) alleles that make up the variable gene complex (haplotype) of the immune system is a large factor. The efficacy of GFDs in Crohn’s patients is likely linked to the HLA-DQ2 and -DQ8 haplotypes, with one study finding that only 12 percent of patients with IBDs and without these haplotypes experienced symptom abatement after six months on a GFD. In contrast, 60 percent of patients with either of the haplotypes experienced symptom abatement. Because 60 percent of Crohn’s patients don’t have either haplotype, these findings suggest that GFDs will not be effective for the majority of patients.

Adjunctive Nutritional Supplementation

Considering the relationship between Crohn’s and gluten, GFDs might be an important part of the puzzle for some patients. However, the shortcomings of these diets and their restrictive nature leave many clinicians and Crohn’s patients searching for better dietary alternatives for managing symptoms not fully addressed by conventional therapies. Nutritional supplementation designed to promote microbiome health presents new possibilities for symptom management for both those using GFDs and those for whom GFDs are ineffective.

Supplements targeting the microbiome seek to restore a healthy balance of bacterial colonies and support optimal function. As a result, nutritional supplementation could be included along with other therapies, including GFDs, to help correct both natural and therapy-induced microbiome disruption, as well as augment other microbiome-supporting therapies. By integrating multiple therapies designed to support microbiome health, Crohn’s patients can address specific symptoms while building resilience against flare-ups caused by a distorted microbiome.

One of the most promising nutritional supplements for Crohn’s patients is butyric acid, a cellular signaling molecule in the GI tract that is deficient in Crohn’s patients. Providing the GI tract’s immune cells with the butyric acid they’re missing helps normalize the microbiome. Evidence suggests this type of supplementation can have significant beneficial effects; one study found that 69 percent of participants responded to bioavailability-optimized orally administered butyrate supplementation, with 53 percent achieving symptom benefit. 

Further research is necessary to more fully understand the potential of butyrate supplementation to address symptoms in Crohn’s disease. However, for now, its use in addition to conventional and non-conventional therapies like GFDs might benefit patients. Other supplements, like fish oil, exist in a similar state, with some evidence in favor of their benefit in Crohn’s, and many questions left to be answered.

The power of Tesseract supplements lies in enhancing palatability, maximizing bioavailability and absorption, and micro-dosing of multiple nutrients in a single, highly effective capsule. Visit our website for more information about how Tesseract’s products can help support your gastrointestinal health.*

Works Cited

Aziz, I., Branchi, F., Pearson, K., Priest, J., & Sanders, D. S. 2015. Inflammatory Bowel Diseases, 21(4):847-853.

Crohn disease exclusion diet after single medication de-escalation (CEASE). 2015. Retrieved February 5, 2018.

Crow, J. 2015. A cross-over trial assessing the impact of a gluten free diet on Crohn’s disease activity.

Herfarth H., Martin F., Sandler S., Kappelman M., Long M. 2014. Inflammatory Bowel Diseases, 20:1194–1197.

Huda-Faujan, N., Abdulamir, A., Fatimah, A., Anas, O. M., Shuhaimi, M., et al. 2010. The Open Biochemistry Journal, 4:53-58.

Karell, K., Louka, A. S., Moodie, S. J., Ascher, H., Clot, F., et al. 2003. Human Immunology, 64(4):469-477.

Kresser, C. (2017). Should you go gluten-free?

Lane, E. R., Zisman, T., & Suskind, D. 2017. Journal of Inflammation Research, 10:63-73.

Sabatino, A. D., Morera, R., Ciccocioppo, R., Cazzola, P., Gotti, S., et al. 2005. Alimentary Pharmacology and Therapeutics, 22(9):789-794.

Staudacher H., Irving P., Lomer M., Whelan K. 2014. Nature Reviews Gastroenterology & Hepatology. 11:256–266.

Al Czap, Founder | Tesseract

Al Czap has more than four decades of professional experience in preventative medicine. He founded Thorne Research in 1984 (sold in 2010) and he published Alternative Medicine Review for 17 years beginning in 1996. AMR was a highly acclaimed, peer-reviewed, and indexed medical journal. Al was the first to recognize the need for hypoallergenic ingredients and to devise methods of manufacture for and delivery of hypoallergenic products to underserved patient populations. His work has greatly impacted those with impaired immune and digestive systems and compromised health due to environmental exposures.

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