In people with celiac disease, eating gluten can wreak havoc on oral health. In fact, eighty-five percent of people with celiac disease have problems with their tooth enamel. And mouth symptoms from eating gluten- especially discolored teeth and canker sores- can be the first signs of celiac to show up in children. Gluten sensitivity may pose a problem for oral health too. There are telltale signs of celiac disease that show up first in the mouth. You don’t want to miss these, especially if you have children. Who could imagine something like wheat gluten would take such a toll on the mouth?

Celiac disease is an autoimmune disease triggered by eating wheat gluten. Gluten is a protein found in wheat, rye, and barley that gives bread its chewy consistency. In celiac disease, when a person eats gluten, the immune system attacks the body and slowly destroys the gut lining, which makes it hard to absorb vitamins and minerals. If it goes untreated, celiac disease can lead to other autoimmune diseases. A gluten-free diet can turn it all around. Approximately 1 in 100 people in the US have celiac disease but some sources say it may be up to 2 in 100. There are many people walking around who don’t yet know they have celiac disease. Eighty-three percent of people with celiac disease are undiagnosed- or even misdiagnosed with the wrong condition. Gluten sensitivity, which we discuss later, is less well understood and may impact 0.6% to 13% of people.

“85% of people with celiac disease have tooth enamel defects.”

Since celiac disease affects the gut and many other systems of the body, its effects spill over into the mouth. The gut and the mouth are kissing cousins, as I explain in my book, Heal Your Oral Microbiome. They share the same lining and structure and immune system. If you have chronic mouth sores, discolored teeth, a swollen, red tongue, dry mouth, or other mouth problems, don’t write off gluten as a possible cause. And be on high alert for these symptoms in children! We will discuss the signs and symptoms to look for, testing, treatments, and how the oral microbiome is imbalanced in celiac disease.

How Does Celiac Disease Affect Your Mouth?

Since mouth symptoms can be the only clues of hidden celiac disease, it’s important to pay attention to the mouth. Teeth enamel defects and canker sores are telltale signs. These are the ways that celiac disease and gluten can harm the mouth…

Celiac Disease Mouth Sores


Celiac disease can cause canker sores or mouth sores, also known as aphthous ulcers. These sores can show up on the inside of your cheeks and cause pain, especially if you eat something sour or salty. Mouth sores are not to be ignored. And don’t write them off thinking that you just ate too much citrus foods. They are telling you something is off with your oral health. Canker sores are common in celiac disease. If your mouth sores don’t resolve easily or keep coming back, it could be that you have undiagnosed celiac disease or that gluten is causing your mouth sores.

Gluten exposure in celiac disease can also cause angular cheilitis mouth sores. These sores can be found at the edge of your mouth, where your lips meet. They can be painful and unsightly cracked sores. Although they might look like cold sores, they are not the same thing.

Mouth sores can also be caused by inadequate B vitamins or other vitamins, which I review in my blog, Vitamins for Oral Health.

Teeth Enamel Problems

One of the most important signs of celiac in the mouth are changes to teeth enamel. Dentists call these “enamel defects” or “hypoplasia.” You’ve seen them. Teeth can be discolored. They may look yellow or brown. Teeth may have white, yellow, or brown spots on them. Celiac disease teeth may show little pits on them or bands across them. Teeth enamel may be mottled or translucent-looking. In celiac disease, teeth are damaged by the immune reaction to eating gluten and the nutritional deficiencies that occur until the person goes on a gluten-free diet.

Eighty-five percent of people with celiac disease have problems with their tooth enamel. For adults, this could mean “bad teeth,” extractions, cavities, and tooth loss. Dry mouth is another symptom of celiac disease, which can change the microbiome in the mouth and encourage cavities in teeth that already have weak enamel.

Celiac Tongue

Swollen, red, smooth tongue (known as atrophic glossitis) can make it painful to swallow and eat. If celiac is affecting the texture and look of your tongue, you will surely notice it. It will have a smooth or slick look to it. You won’t see the characteristic little bumps or the crease that goes down the middle of the tongue. Geographic tongue, which earns its name because the tongue has shapes on it like a world map, is more common in celiac disease. Geographic tongue is caused by inflammation but is considered harmless.

Mouth Lining Inflammation

Your dentist or hygienist might notice you have inflammation of your oral mucosa or mouth lining. Known as oral lichen planus, it can appear as white patches, redness, or swelling. It might be noticeable as a lacy network on the inside of your cheeks. Your mouth lining may feel painful, uncomfortable, or like its burning. There may be open sores. While many sources say there is no cure, they may not be investigating the root causes of inflammation, such as gluten exposure in someone who has celiac disease or who is gluten-intolerant.

Oral Cancers

Celiac disease patients who are not strictly avoiding gluten get more head and neck cancers than those who are following the gluten-free diet. These are more common in untreated celiac disease: mouth cancer, esophageal cancer, larynx cancer, and lymphoma. The risk is estimated to be 10x higher in people with celiac disease who do not follow a gluten-free diet, compared to those that do.


Gluten and Mouth Symptoms in Children

Problems with teeth and mouth sores might be the most important to recognize in children. These symptoms can make the difference between early detection of celiac versus missed diagnosis. Earlier detection means earlier treatment and fewer long-term side effects. Children can show telltale changes to tooth enamel if they have celiac disease. Sometimes the only symptom in a child with celiac disease is an enamel defect. That’s why dentists, dental hygienists, and pediatricians should be on high alert for discolored or yellow teeth in children.

Children with celiac who are eating gluten will have delayed tooth eruption or they will cut teeth later than most kids. They will be more prone to cavities than other children because their tooth enamel isn’t as strong. Parents, dentists, and pediatricians should be on high alert for these oral health problems in children.

These Mouth Symptoms Could be a Sign of Celiac Disease in Children:1

  • Burning tongue
  • Delayed tooth eruption
  • Dry mouth
  • More cavities than other children
  • Mouth sores (aphthous stomatitis and/or angular cheilitis)
  • Red, slick, tongue (atrophic glossitis)
  • Yellow teeth or discolored teeth


Can Gluten Intolerance Affect Your Mouth?

Mouth symptoms may not just be a problem for people with celiac. Gluten sensitivity is a related condition that may also hold back oral health. Known officially as non-celiac gluten sensitivity, people with this condition get symptoms after eating gluten such as bloating, gas, diarrhea, abdominal discomfort, but they don’t have full-blown autoimmune celiac disease. It isn’t known how many people have gluten sensitivity because it is hard to diagnose, but it has been estimated to affect 0.6% to 13% of the general population.2

Mouth symptoms in gluten sensitivity are not so commonly or widely reported as in celiac. However, people with gluten intolerance can have mouth ulcers or canker sores (called aphthous stomatitis). And if your mouth is giving you trouble with ulcers, geographic tongue, or if your teeth are prone to cavities, it is worth looking into gluten as the culprit. Gluten is a molecule that damages the cells of the mouth lining and gut lining, causing permeability or leakiness in all people. For that reason, it may not be a friend to the mouth for many people, not just those who have celiac or gluten intolerance.3

The Oral Microbiome, Gluten, and Celiac Disease

Celiac disease affects the gut microbiome. The gut microbiome can be out of balance, or dysbiotic, when people with celiac are eating gluten. Usually, they show lower levels of good bacteria and higher levels of potentially pathogenic bacteria when compared to healthy people. However, when people with celiac disease start a gluten-free diet, their gut microbiomes change significantly. For this reason, it is believed that gut bacteria may be involved in celiac disease, the inflammation it causes, and its effects on the gut lining.

In the celiac disease mouth, there are very different oral bacteria communities than in the mouths of healthy subjects. They particularly show abnormally high levels of lactobacilli.4

There can be lower diversity in the oral microbiome of adults with celiac disease while Neisseria species and Proteobacteria are more abundant. In children, Streptococcus mutans and lactobacilli colonies were lower in children with celiac disease, who also showed teeth enamel defects and recurrent mouth sores. Other studies showed that even after beginning a gluten-free diet, children’s oral microbiomes don’t always return to balance.5

Certain mouth bacteria can degrade gluten.6 These include Rothia mucilaginosa, Rothia aeria, Actinomyces odontolyticus, Streptococcus mitis, Streptococcus sp., Neisseria mucosa, and Capnocytophaga sputigena. Rothia species were especially good at breaking down gluten. These microbes, and Lactobacillus species could play a role in the immune response seen in celiac disease.7 It also presents the possibility that oral bacteria could be a therapy for mouth symptoms in celiac disease.

Best Tests for Celiac Disease and Gluten Sensitivity

The accepted blood test for celiac disease measures total immunoglobulin A (IgA), IgA anti-gliadin antibody, and IgA tissue transglutaminase antibody in serum.  This type of test may be covered by your insurance plan, depending on your diagnosis. It’s usually followed up by the “gold standard” small intestinal tissue biopsy, which takes little pieces of the small intestinal lining during an endoscopy. The test looks for the characteristic gut lining damage seen in celiac disease, called “villous atrophy.” Genetic blood tests for HLA-DQ2 and or HLA-DQ8 can tell you your risk of celiac disease. These genotypes are carried by nearly all patients with celiac disease.

A very affordable and simple solution is to do an elimination and challenge. Eliminate gluten completely from your diet for one month or more and watch your symptoms. If you notice that mouth sores are less frequent or that your tongue is more comfortable, give it two more months. To reintroduce gluten, eat 10-20 grams of gluten-containing foods for a couple of days in a row and watch for mouth symptoms. If gluten is a problem, you should notice it pretty quickly. Other doctors do variations on this protocol.

Treatment for Celiac Mouth Symptoms

Gluten-free Diet for Oral Health

The most important treatment for celiac disease is a strict gluten-free diet. It isn’t a fun dietary change but it’s necessary to turn off inflammation and the autoimmune attack that happens in celiac disease. There are many gluten-free alternatives and you can use the help of a functional medicine health coach to get your diet all dialed in. Be aware that gluten is in many foods that are not labeled as containing it. Because it is so difficult to completely take out of the diet, there is a diet called the Gluten Elimination Contamination Diet to address even trace levels of gluten.8 Eating gluten-free can be very satisfying and delicious!

A gluten-free diet decreases canker sores in people with celiac disease. Going on a gluten-free diet improves teeth, but it can’t reverse earlier damage. That’s why detecting it early is critical. For adults with celiac disease diagnosed later in life, the tooth damage prior to going on a gluten-free diet may be permanent.

Aside from gluten-free food and beverages, people with celiac disease or gluten intolerance have to be vigilant about gluten exposure elsewhere. Dental hygiene products such as floss, toothpaste, and mouthwash should be gluten free. Ask your dentist and hygienist to use gluten-free dental products when you get your checkup.

Test and Improve the Oral Microbiome

Balancing the microbiome could help to improve the mouth and immune system symptoms. Indeed, probiotics have been shown to affect celiac disease in animal studies. Consider dental probiotics and prebiotics.

Mouth bacteria and gut bacteria are out of balance in celiac disease. Use cutting-edge tests to measure the oral microbiome and the gut microbiome. Balance those populations with the help of a functional medicine practitioner.

Heal the Mouth Lining

Nourish the oral lining and encourage tissue healing with L-glutamine, aloe vera juice, slippery elm, and zinc carnosine.

Don’t Miss These Important Mouth Symptoms That Point to Celiac Disease

While mouth sores, teeth enamel problems, and geographic tongue can be caused by other things, celiac or gluten sensitivity is something to seriously consider and rule out when looking for the root cause of your mouth problems. Since more than 83% of patients with celiac disease are walking around undiagnosed or misdiagnosed with other conditions, the signs and symptoms that show up in the mouth should not be ignored. It’s all the more important for children, who may show enamel defects as the only clue to “silent” celiac disease. If you or your child has unexplained stubborn oral health problems, a gluten-free elimination is certainly worth a try!


  1. Macho VMP, Coelho AS, Veloso ESDM, de Andrade DJC. Oral Manifestations in Pediatric Patients with Coeliac Disease – A Review Article. Open Dent J. 2017;11:539-545.
  2. Roszkowska A, Pawlicka M, Mroczek A, Balabuszek K, Nieradko-Iwanicka B. Non-Celiac Gluten Sensitivity: A Review. Medicina (Kaunas). 2019;55(6).
  3. Fasano A, Sapone A, Zevallos V, Schuppan D. Nonceliac gluten sensitivity. Gastroenterology. 2015;148(6):1195-1204.
  4. Tian N, Faller L, Leffler DA, et al. Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients. Applied and environmental microbiology. 2017;83(6).
  5. Francavilla R, Ercolini D, Piccolo M, et al. Salivary microbiota and metabolome associated with celiac disease. Applied and environmental microbiology. 2014;80(11):3416-3425.
  6. Fernandez-Feo M, Wei G, Blumenkranz G, et al. The cultivable human oral gluten-degrading microbiome and its potential implications in coeliac disease and gluten sensitivity. Clin Microbiol Infect. 2013;19(9):E386-394.
  7. Poddighe D, Kushugulova A. Salivary Microbiome in Pediatric and Adult Celiac Disease. Frontiers in cellular and infection microbiology. 2021;11:625162.
  8. Leonard MM, Cureton P, Fasano A. Indications and Use of the Gluten Contamination Elimination Diet for Patients with Non-Responsive Celiac Disease. Nutrients. 2017;9(10).


Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.