Celiac.com 05/20/2026 - It is not uncommon for people with celiac disease to have ongoing digestive symptoms or other health issues, even after starting a gluten-free diet. Although celiac disease is better understood than ever, much remains to be learned about how the disease affects the body, how long healing takes, and why some symptoms may continue after gluten is removed from the diet. One study explains why digestive issues may linger for years, even after going gluten-free.
Not everyone with celiac disease who begins a gluten-free diet will recover quickly or completely. According to one study:
- "After an average of 11 months on a gluten-free diet, 81% of patients with celiac disease and positive tissue transglutaminase IgA (tTG-IgA) at baseline will revert to negative tTG-IgA (SOR: C, disease-oriented evidence from retrospective cohort study). The intestinal mucosa of adult patients with celiac disease will return to normal after following a gluten-free diet for 16 to 24 months in only 8% to 18%. However, in children after 2 years, 74% will have a return to normal mucosa (SOR: C, disease-oriented evidence from longitudinal studies)."
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This article is intended to help people with celiac disease understand possible reasons for ongoing symptoms and to identify issues they may want to discuss with a qualified health care provider. It is not medical advice. Please consult a physician for diagnosis, treatment, testing, or any medical questions related to celiac disease or any condition mentioned here.
Celiac Disease Follow Up Treatment
Follow-up care is important after a celiac disease diagnosis. Some tests are recommended soon after diagnosis, while others may be repeated over time to monitor healing, nutrition, and related autoimmune conditions.
Blood work for vitamin and mineral deficiencies
Micronutrient deficiencies are common in adults with celiac disease, as are vitamin and mineral deficiencies.
The most common vitamin and mineral deficiencies in celiac patients include B vitamins, especially B12; vitamin A; vitamin D; vitamin E; vitamin K; iron; calcium; carotene; copper; folic acid; magnesium; selenium; and zinc.
Celiac Disease and Ongoing Symptoms After a Gluten-Free Diet
Most people with celiac disease experience a major improvement in symptoms within weeks or months of starting a gluten-free diet. However, some continue to have digestive problems, fatigue, nutrient deficiencies, pain, or other symptoms. Others may improve at first and then relapse. When symptoms continue, the most important first step is to look carefully for common and treatable causes.
Hidden Gluten Exposure
New research shows that most people with celiac disease are regularly exposed to gluten, even when they are trying to be careful. For many people with celiac disease, gluten exposure is usually ongoing and silent. This article explores how much gluten exposure do celiacs get on a gluten-free diet. It is also important to remember that celiac patients are really bad at judging gluten-exposure based on symptoms.
People with ongoing symptoms should review possible sources of gluten exposure, including restaurant meals, shared kitchens, cross-contact, medication binders, supplements, cosmetics used near the mouth, and misunderstandings about the strictness required by the gluten-free diet. Repeat blood tests may help identify continued gluten exposure, but they may not be sensitive enough to detect low-level or intermittent exposure.
Some people with celiac disease report positive results after taking AN-PEP enzymes, such as GliadinX is a brand that we've reviewed, before meals when eating outside the home. These enzymes have been shown in multiple studies to break down small amounts of gluten in the stomach before it reaches the intestines. They are not a substitute for a gluten-free diet, but some people use them as an added precaution against accidental exposure.
Lactose Intolerance
The enzymes needed to digest lactose are produced by the intestinal villi, which can be damaged by gluten exposure in people with celiac disease. As a result, many people with newly diagnosed or active celiac disease have trouble digesting milk and other lactose-containing foods. In some cases, this improves as the intestine heals.
Many people with celiac disease also report problems with casein, a protein found in dairy products. Lactose intolerance is a common misdiagnosis in celiac patients, because gluten-related mucosal damage can temporarily leave them unable to digest lactose-containing products.
Testing for lactose intolerance can be done with a hydrogen breath test, often called a Lactose H2 breath test. Treatment may include avoiding lactose temporarily, using an over-the-counter lactose enzyme when eating dairy, or reintroducing dairy carefully as healing progresses. Re-colonizing the small intestine with beneficial bacteria may also help. How is lactose intolerance related to celiac disease?
FODMAPS
FODMAPs is short for "fermentable oligosaccharides, disaccharides, monosaccharides and polyols." These are carbohydrates found in many common foods that are poorly absorbed by some people. When FODMAPs are not well absorbed, they can cause bloating, gas, abdominal pain, diarrhea, constipation, and other symptoms that can resemble celiac disease symptoms.
A low FODMAP diet has been shown to help reduce symptoms of IBS, and it may be helpful for some people with celiac disease who continue to have symptoms despite a strict gluten-free diet. FODMAPs have also been shown to play a role in non-celiac gluten sensitivity (NCGS). A new app can help people zero in on FODMAPs in food. Related articles include: Can Low FODMAP Diet App Help Some Celiac and IBS Patients?; What's the Deal with FODMAPs and Gluten-sensitivity in IBS?; and FODMAPs, Food Intolerance and You.
Fiber
A recent study indicates that inulin fiber may speed celiac disease recovery. One of the most important discoveries was that people with celiac disease had a reduced ability to process fiber in the small intestine. This was true both for people newly diagnosed with celiac disease and for people already following a gluten-free diet.
Because fiber was not being processed as efficiently, people with celiac disease produced lower levels of beneficial compounds created during fiber digestion. This does not mean every person with celiac disease should immediately add large amounts of fiber, because some people are sensitive to certain fibers or FODMAPs. However, it does suggest that fiber quality, gut bacteria, and small intestinal healing may all be important parts of recovery.
Beneficial Bacteria
Probiotics may help some people restore a healthier balance of intestinal flora. Products with multiple types of bacteria may be useful, and refrigerated products often contain higher levels of live bacteria. Kefir, raw kimchee, and raw sauerkraut may also contain active cultures, though people with celiac disease should always confirm that any product is gluten-free and tolerated.
Related articles include: Celiac Disease Onset Changes Gut Microbiota in Children; What Can Gut Microbiomes Teach Us About Gastrointestinal Distress in Children?; and Gut Microbiota Reflects Disease Severity in COVID-19 Patients.
Small Bowel Bacterial Overgrowth
Small bowel bacterial overgrowth, sometimes called SIBO or SBBO, can cause bloating, gas, diarrhea, abdominal discomfort, nutrient problems, and other symptoms that overlap with celiac disease. In a report published in the American Journal of Gastroenterology, Vol. 98, No. 4, 2003, 10 of 15 people with continuing symptoms showed evidence of bacterial overgrowth within the small bowel.
Testing may include lactulose hydrogen breath testing. Suggested treatment in that report included the non-systemic prescription antibiotic rifaximin, 800 mg per day for one week. Note that the antibiotic is called Rifaximin in England and Xifaxan in the U.S. Digestive function should also be evaluated as a possible underlying cause of SBBO. For more information, see Breath Tests for the Non-invasive Diagnosis of Small Intestinal Bacterial Overgrowth: A Systematic Review With Meta-analysis, and Rosacea and Small Intestinal Bacterial Overgrowth (SIBO).
Other Food Sensitivities
Some people with celiac disease may have additional food sensitivities. An IgG sensitivity is different from the IgE allergies most allergy doctors check for. Commonly reported food sensitivities include dairy casein, corn, soy, and eggs. Some people improve by avoiding the food for a time and using food rotation. Food sensitivities may also lessen as digestion and intestinal health improve.
An elimination diet can help identify foods that may be contributing to symptoms. One approach is to start with the most common food allergens, eliminate one at a time for 2-3 weeks, then add the food back and record any symptoms. It may make sense to begin with the following:
- Milk
- Eggs
- Peanuts
- Tree nuts, such as almonds, cashews, and walnuts
- Soy
- Fish
- Shellfish, such as shrimp, crab, and lobster
- Sesame seeds
- Mustard
Dr. Fasano has created a diet for those with celiac disease that appears to help many people improve quickly. The Autoimmune Protocol Diet is even more strict than the Fasano Diet, and some people may need a stricter approach to fully recover. There has also been increased focus on FODMAPS, since a low FODMAP diet has been shown to help reduce IBS symptoms. This older article also has some interesting ideas.
Artificial Sweeteners
Most artificial sweeteners and sugar alcohols are technically gluten-free, they can still trigger digestive symptoms in people with celiac disease or gluten sensitivity, including bloating, gas, and diarrhea.
Gluten risk usually comes not from the sweeteners themselves, but from cross-contact or other ingredients in processed foods. Careful label reading and choosing certified gluten-free products can help reduce risk. Sweeteners discussed in the linked article include advantame, acesulfame potassium (Ace-K), aspartame, cyclamate, erythritol, hydrogenated starch hydrolysates (HSH), isomalt, lactitol, maltitol, mannitol, neotame, saccharin, sorbitol, stevia, sucralose, and xylitol. Individual tolerance varies, and some sweeteners may also affect gut bacteria or cardiovascular health, so moderation and symptom awareness are especially important.
Digestive Function
Continuing symptoms may be related to more than one digestive problem. A complete evaluation may be helpful, especially when symptoms persist despite a strict gluten-free diet. In some cases, a comprehensive stool analysis may be obtained by mail and by prescription.
Digestive Enzymes
Pancreatic enzymes may assist with more complete digestion and may discourage unhealthy bacterial growth. Many people with celiac disease prefer vegetable-based enzymes, which may be purchased online or at health food stores. Animal-derived enzymes are available by prescription.
People who try digestive enzymes often experiment carefully to see what works best. To reduce the chance of heartburn, some people start by sprinkling half of a capsule on food and increasing as needed and tolerated. Be sure any enzymes used are gluten-free. Watch out for maltase, which can sometimes be made from barley. Related articles include: Are Gluten-Busting Enzymes the Best Hope for Future Celiac Treatment and Maintenance?; Could Enzymes from Oral Bacteria Treat Celiac Disease?; Researchers Review Potential of Gluten Degrading Enzymes for Treatment of Celiac Disease; and Imagine a Gluten-Busting Enzyme that Worked Like LactAid.
Carbohydrate Intolerance
Some people do not digest carbohydrates and sugars well. Undigested carbohydrates can encourage the growth of unwanted yeasts and bacteria and may contribute to gas, bloating, diarrhea, or abdominal pain. More information on a diet low in carbohydrates may be found in the book "Breaking the Vicious Cycle" by Gottschall, who recommends eliminating complex carbohydrates to reduce the growth of "bad" bacteria.
Intestinal Motility
Increased intestinal motility may contribute to continuing diarrhea. Some people try reducing motility by using a fiber supplement such as Benefiber or Citrucel. People who have had their gall bladder removed may want to ask their doctor about bile salt-related diarrhea. In some cases, Cholestid, a prescription drug used for lowering cholesterol, may also slow motility by binding irritating bile salts.
Decreased Stomach Acid
Low stomach acid, also called hypochlorhydria, may interfere with digestive enzymes and may promote yeast or bacterial overgrowth. A useful source of information is the book "Why Stomach Acid is Good for You" by Wright and Lenard. Testing may include the Heidelberg Capsule or Gastrocap tests.
Some people with celiac disease and low stomach acid report benefits from supplemental Betaine HCl, bitters, digestive enzymes, and probiotics, available at health food stores. Related articles include: Reduced Fecal Acidity Mirrors Rise in Celiac Rates.
Autoimmune Gastritis
This study demonstrates that autoimmune gastritis affects roughly one in ten people with celiac disease. People with moderate intestinal changes, known as Marsh type 2, and without typical celiac antibodies may be at the greatest risk.
Because both celiac disease and autoimmune gastritis can cause nutrient deficiencies and anemia, identifying and treating autoimmune gastritis in celiac patients can be important for long-term health.
Helicobacter Pylori
A study by Villanacci, et al., published 8/28/2006 in the American Journal of Gastroenterology, noted that 44% of people diagnosed with celiac disease tested positive for Helicobacter pylori at the time of, or within one year of, their celiac disease diagnosis. Interestingly, patients with helicobacter pylori colonization have a decreased risk of celiac disease. An Iranian study also showed a connection between helicobacter pylori and celiac disease.
Yeast Overgrowth
Some people report continuing symptoms due to yeast overgrowth. Testing may include blood antibody testing for Candida. Suggested treatment has included half a teaspoon of Nystatin powder mixed with water twice daily, and 200 mg Ketoconazole once daily for 2-3 months. Monthly liver function testing during treatment is recommended. Nystatin powder may be ordered by prescription through pharmacies that offer custom compounding.
Digestive function should also be evaluated as a possible underlying cause of yeast overgrowth. Dietary changes may also be considered.
Oxalate Sensitivity
Oxalate sensitivity can cause symptoms in some people due to difficulty metabolizing oxalates, which are naturally occurring compounds found in many foods. When oxalates accumulate, they can form crystals that deposit in tissues and may contribute to inflammation and pain.
Oxalate issues are often linked to kidney stones, but they may also affect the gut, joints, and other tissues, especially in people with compromised gut health or certain genetic tendencies. Symptoms may include joint pain, digestive issues, and chronic fatigue. Sensitive individuals may benefit from discussing oxalate intake with a health care provider or dietitian.
Lectin Sensitivity
Lectin sensitivity may contribute to inflammation in some individuals. Lectins are proteins found in many plant foods, including beans, legumes, and grains. They can bind to carbohydrate molecules on cell surfaces, including cells in the gut lining.
In sensitive people, lectins may irritate the gut barrier and contribute to increased intestinal permeability, often called "leaky gut." This may trigger immune activity and symptoms such as digestive problems, joint pain, or fatigue. Reducing high-lectin foods may help some people, though this should be done thoughtfully to avoid unnecessary dietary restriction.
Cross-Reactivities for Celiac Patients
A recent study indicates that Silicon Dioxide (Food additive E551) May Trigger Intestinal Damage and Inflammation in People with Celiac Disease or Gluten Sensitivity. Cross-reactivity between anti-gliadin antibodies and certain spice proteins indicates that patients with celiac disease or wheat allergy may also react to some spices, even when those spices are gluten-free.
Some spices can also be a source of cross-contact, especially if wheat flour is used as an anti-caking agent. This article explores the topic in more detail:
Parasites and other Bacterial Problems
People with celiac disease can still have unrelated infections or parasites that cause diarrhea or other digestive symptoms. Possible causes include Giardia lamblia, Ascaris lumbricoides, and other bacterial or parasitic problems. Having celiac disease does not rule out the same infections or digestive bugs that can affect anyone else.
Thyroid Screening
Because celiac disease is linked to autoimmune thyroid disease, thyroid screening is recommended for newly diagnosed celiac disease patients. Patients taking thyroid replacement or other medications may need more frequent monitoring and possible dosage adjustment as intestinal absorption improves.
Bone Density Scan
Up to 75% of celiac patients have low bone mineral density. Because of this, bone density scans are recommended for newly diagnosed celiacs. Bone health may improve as the intestine heals and nutrient absorption improves, but monitoring can help identify people who need additional care.
Liver Enzymes
Research from Stanford University School of Medicine's Celiac Management Clinic has noted continued absorption problems in many people who are on a gluten-free diet. A 72-hour quantitative fecal fat test and a 25-gram xylose sugar absorption test can help diagnose continued absorption problems.
Healing progress on the gluten-free diet may be monitored by re-testing whichever diagnostic blood test was initially highest, usually at intervals of 6-12 months. Children are likely to heal within a few months; adults may take a few years, and some may never totally heal.
Calcium and iron status will improve in many people, even without supplements, once the gut heals. Some doctors recommend not prescribing drugs such as Fosamax and Evista until after the intestine heals and more calcium is being absorbed from the diet.
Other Autoimmune Diseases
A number of autoimmune conditions are associated with celiac disease. At least one in three people diagnosed with adult celiac disease will also have another autoimmune disease. Many report significant improvement in other autoimmune conditions after beginning a gluten-free diet. However, some people with celiac disease may develop other autoimmune diseases even after beginning a gluten-free diet.
Conditions to watch for include type 1 diabetes, liver disease, thyroid disease, pancreatic disease, adrenal disease, peripheral and central nervous system problems, connective tissue disease, and other rheumatoid or inflammatory conditions. Related articles include: Celiac Disease is Linked to Autoimmune Thyroid Disease; and The Ten Risk Factors Most Associated with Celiac Disease.
Article originally published 03/25/2007, updated 04/07/2021 and 05/20/2026.
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