I am sorry you are still experiencing symptoms. You are definitely not alone. It is estimated that about 7-30% of people with celiac disease still have GI symptoms even though they have followed a gluten-free diet for at least 12 months, this is referred to as non-responsive celiac disease. (1)

Here are the most common causes of not getting better after diagnosis:

  • Continued exposure to gluten
  • Lactose intolerance
  • Fructose malabsorption (Not to be confused with fructose intolerance which is a hereditary condition)
  • Difficulty digesting FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols)
  • Small intestinal bacterial overgrowth (SIBO)
  • Other food allergies/intolerances
  • Exocrine pancreatic insufficiency
  • Microscopic colitis
  • Refractory celiac disease (very rare, only 1-2% of people with celiac disease) (1,2)

Exposure to Gluten

One of the most common causes for persistent symptoms is continued exposure to gluten. This can be due to dietary indiscretion, as well as inadvertent exposure. Staying gluten-free can be a challenge as so many foods contain gluten. In addition, the amount that can make someone with celiac disease sick is very small. In a study, researchers found that some patients with celiac disease reacted to as little as 10 mg a day of gluten – that is just crumbs! (3)

Dietary Indiscretion:

It is very important to always stay gluten-free to allow the body to recover and heal, as well as avoid further complications. Being strictly gluten-free for celiac disease does not include eating gluten occasionally. Common situations of dietary indiscretion:

  • Eating gluten when tempted.
  • Being on a “low gluten diet.”
  • Eating” just a bite” and tasting foods with gluten.
  • Eating gluten because of peer pressure/being embarrassed and wanting to be like everyone else (common with kids and teens).
  • Eating gluten at holidays and celebrations.

Inadvertent exposure:

There are many opportunities for inadvertent exposure. Here are the most common pitfalls:

  • Not reading labels carefully (ingredients frequently change).
  • Exposure to “background levels of gluten.” A study found that 8% of food samples of those eating gluten-free tested positive for gluten, and 66% of participants had at least one sample positive for gluten. Most did not notice the exposure. Gluten was found in all types of foods, even foods labeled gluten-free. (4)
  • Eating out is another high-risk area of exposure. In a study of 105 patients with celiac disease 29% of gluten exposure was attributed to problems ordering at restaurants. (5)
  • Cross-contact in meal preparation at home.
  • Eating oats that have had cross-contact with gluten. If you eat oats read our information on oats: Oats on the Gluten Free Diet.  Always check with your doctor if it is ok to consume oats. Another issue with oats apart from cross-contact is that a small subset of people with celiac disease will react to the protein in oats (avenin) and will get similar symptoms to celiac disease. Because of this, many doctors recommend to only introduce oats once you are stable on the gluten-free diet and antibody levels have normalized.

The best way of dealing with exposure to gluten is reviewing the gluten-free diet with a registered dietitian (RDN) skilled in the gluten-free diet and have regular follow-ups with your doctor/gastroenterologist to monitor your celiac specific antibody levels.

The best way of dealing with exposure to gluten is reviewing the gluten-free diet with a registered dietitian (RDN) skilled in the gluten-free diet and have regular follow-ups with your doctor/gastroenterologist to monitor your celiac specific antibody levels.

Conditions That May Cause Continued GI Symptoms
ConditionDescriptionCommon SymptomsDiagnosisTreatment
Lactose intoleranceLack of lactase enzymeGas, bloating, diarrhea, cramps, constipation, nausea/vomitingHydrogen breath testLactose tolerance testLimit foods that are high in lactose
Fructose malabsorptionUnable to absorb fructose properly causing fructose to be fermented in the large intestineGas, bloating, cramps, diarrheaHydrogen breath testElimination dietLimit foods high in fructoseLow FODMAP diet can sometimes be helpful
FODMAP sensitivityDifficulty digesting carbohydrates high in FODMAPs – fermentable oligosaccharides, disaccharides, monosaccharides and polyols Gas, bloating, diarrhea, constipation, crampsElimination dietLimit foods that are high in FODMAPs, (usually short-term) 
Other food sensitivities and allergies.Immune reaction to certain foods, common ones are: dairy, soy and cornGas, bloating, diarrhea, rashes, itchingAllergy testingFood sensitivity testingElimination dietEliminate food from diet that is causing reaction.
SIBOOvergrowth of bacteria in the small intestineGas, bloating, diarrhea, constipationHydrogen (lactulose) breath test to measure hydrogen and methane gases AntibioticsProbioticsSometimes a low FODMAP diet is recommended short-term.Meal spacing (6)
Exocrine Pancreatic InsufficiencyInsufficient pancreatic digestive enzymesGas, bloating, abdominal pain, steatorrhea (oily stool), weight loss, nutrient deficienciesFecal elastase test72- hour fecal fat testPancreatic function testPancreatic enzyme replacement therapyVitamins A,D,E,K supplementation if indicated (7)
Microscopic colitisInflammation of colonWatery diarrhea, abdominal pain, cramping, gas, bloating, nausea, dehydrationColonoscopy or flexible sigmoidoscopy with biopsyLow fat and low fiber diet.Dairy free dietMedications such  as steroids, anti-inflammatories, bile acid blockers, TNF inhibitors (8)
Refractory celiac diseasePersistent villous atrophy and malabsorption despite strict gluten-free diet for at least 12 months (1)Villous atrophyMalabsorptionDiarrheaWeight loss  Strict gluten-free diet.SteroidsNutritional supplements to address any deficiency (1)

Healing Time

I also want to note that healing time is very individual. Once gluten is removed from the diet healing starts within days, but can take months and even years for some. Although gradual healing does not usually exceed 2 years (9). It is important that you go to regular follow-ups with your gastroenterologist to monitor your healing. Usually doctors will follow-up within 6 months of diagnosis to check that antibody levels are normalizing and confirm that the diet is working. Sometimes an endoscopy is done one year after diagnosis to check for healing.  After the initial year annual follow-ups are usually recommended.

A Note About Fiber

Another thing to keep in mind is that gluten-free foods are generally higher in starch and lower in fiber. This can cause problems for some with symptoms such as constipation, gas and bloating.

How to increase fiber in the gluten-free diet:

Eat less processed gluten-free foods and more gluten-free whole foods and whole grains. Just make sure they are labeled gluten-free as many have had cross-contact with gluten-containing grains. Focus on nutritious gluten-free whole grains such amaranth, buckwheat, millet, sorghum, teff, quinoa. Also, eat plenty of fruits and vegetables! Fresh fruits and veggies are naturally gluten-free and rich in fiber, aim for 10 servings a day. Nuts, seeds and legumes are also great sources of fiber. Note that legumes have a risk of cross-contact with gluten-containing grains, so always pick through them before soaking, even if they are labeled gluten-free.

If you are experiencing symptoms all of the above should be discussed with your celiac specialist/healthcare provider. I recommend seeing someone who specializes in celiac disease as they are familiar with the complications and disorders related to celiac disease:

How to find a gastroenterologist or dietitian that specializes in celiac disease:



  1. Kelly CP, Bai JC, Liu E, Leffler DA. Advances in diagnosis and management of celiac disease. Gastroenterology. 2015;148(6):1175-86.
  1. National Celiac Association (NCA). Going Gluten-Free: Off to a Fresh Start. Presentation. Updated October 2020.
  1. Catassi C, Fabiani E, Iacono G, D’Agate C, Francavilla R, Biagi F, Volta U, Accomando S, Picarelli A, De Vitis I, Pianelli G, Gesuita R, Carle F, Mandolesi A, Bearzi I, Fasano A. A prospective, double-blind, placebo-controlled trial to establish a safe gluten threshold for patients with celiac disease. Am J Clin Nutr. 2007 Jan;85(1):160-6.
  1. Silvester JA, Comino I, Kelly CP, Sousa C, Duerksen DR; DOGGIE BAG Study Group. Most Patients With Celiac Disease on Gluten-Free Diets Consume Measurable Amounts of Gluten. Gastroenterology. 2019 Dec 19. pii: S0016-5085(19)41945-8. doi: 10.1053/j.gastro.2019.12.016. [Epub ahead of print] PubMed PMID: 31866245
  1. Silvester JA, Graff LA, Rigaux L, Walker JR, Duerksen DR. Symptomatic suspected gluten exposure is common among patients with coeliac disease on a gluten-free diet. Aliment Pharmacol Ther. 2016;44(6):612-619. https://www.ncbi.nlm.nih.gov/pubmed/27443825 Accessed January 4, 2020.
  1. Small intestinal bacterial overgrowth. BIDMC Website:  https://www.bidmc.org/centers-and-departments/digestive-disease-center/services-and-programs/celiac-center/celiacnow/nutrition-and-the-gluten-free-diet/nutritional-considerations-on-the-gluten-free-diet/small-intestinal-bacterial-overgrowth/level-3#:~:text=SIBO%20is%20a%20clinical%20diagnosis,way%20to%20diagnose%20SIBO%20currently.
  1. Struyvenberg MR, Martin CR, Freedman SD. Practical guide to exocrine pancreatic insufficiency – Breaking the myths. BMC Med. 2017 Feb 10;15(1):29. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5301368/
  1. Mayo Clinic. Microscopic Colitis. Mayo Clinic Website: https://www.mayoclinic.org/diseases-conditions/microscopic-colitis/symptoms-causes/syc-20351478
  1. Lebwohl B, Murray JA, Rubio-Tapia A, Green PH, Ludvigsson JF. Predictors of persistent villous atrophy in coeliac disease: a population-based study. Aliment Pharmacol Ther. 2014 Mar;39(5):488-95. doi: 10.1111/apt.12621. Epub 2014 Jan 16. PMID: 24428688; PMCID: PMC4012428.

Reviewed October 21, 2022.