Celiac with Persistent Symptoms? Here’s why.

Celiac with Persistent Symptoms? Here’s why.

Fact: 47% of people on a gluten free diet still have gut symptoms one year post celiac diagnosis (1). 

That is a large statistic. Often after a diagnosis, people feel a lot of emotions. Relief at finally finding out what is wrong, overwhelmed at the life impact of this disease and hope that symptoms will soon improve. For many people certain symptoms can improve, for example neurological symptoms like brain fog can start to improve within a couple weeks. For other people, bothersome gut symptoms can persist despite being on a gluten free diet. This is frustrating!

This article will address some reasons why persistent symptoms can happen to people with celiac disease on a gluten free diet.

1. Time

On average, it takes 10-12 YEARS to receive a celiac disease diagnosis. It’s no wonder that by the time diagnosis occurs there usually extensive damage to the intestinal lining. How long does it take to see healing of the lining? A week? A couple months? Research (2, 3) is actually showing:

It takes an average of two YEARS to see complete healing of the intestinal lining post celiac diagnosis. 

Two years, you read that correctly. This healing time depends on a number of factors: age (young people heal much faster than elderly), extent of damage at diagnosis and if you are male or female. Does it mean it takes that long to see reversal of symptoms? Nope. For the majority of people, symptoms start improving within weeks. Digestion related symptoms may take more time. The lining of the gut is exquisitely intricate and very complex. It needs time and a gluten free environment to fully heal. To fresh your knowledge on celiac disease in simple terms, read more here.

2. Non-responsive celiac disease or refractory celiac disease

Of the people that are on a strict gluten free diet, up to 30% will have persistently elevated celiac specific antibodies, symptoms and intestinal villi damage at one year post diagnosis (4). This persistent gut damage could be from gluten cross contamination, non-responsive celiac disease or refractory celiac disease. For most people, the issue is that gluten is sneaking in some how.

Careful attention MUST be paid to keeping food safe. 1/100 of a slice of bread is enough to cause persistent damage to the gut. That’s crumbs. To put it in perspective, in order for a food manufacturer to label their product as gluten free it must test below 20 part per million. What does that look mean?

20 ppm of gluten is like 1/2 teaspoon in a 125 L bathtub or 20 cents in $10,000. 

Often people aren’t aware about how careful they need to be about cross contamination. Read more about what actually happens when someone with celiac disease eats gluten here. Or view my getting started guide to learn more about how to improve your kitchen for safety and eating safely.

Once it’s clear that there is no cross contamination happening, the symptoms may be classified as non-responsive celiac disease. This more sensitive form of celiac disease is characterized by persistent damage to the gut despite eating a carefully gluten free diet. The treatment for this is a gluten contamination elimination diet. Under the care of a skilled dietitian, this diet removes any chance of cross contamination for three months. This treatment is effective in the majority of people with non-responsive celiac and they can normally resume a normal gluten free diet. The other small percentage may have refractory celiac disease (damage persists despite no gluten contamination) and need to be treated further by their doctor with immune suppressant medication. (5)

celiac disease, persistent symptoms, IBS, registered dietitian, gluten intolerance

3. Underlying medical issues

In some people with celiac disease or gluten intolerance there may be other medical issues that may be contributing to persistent gut issues. If you have a gut feeling that something else is wrong, advocate for yourself and speak with your doctor about this.

If you feel something is wrong, speak up.

Possible medical issues that can be associated with celiac disease are functional gastrointestinal disorders, IBS, SIBO (small intestinal bacteria overgrowth), microscopic colitis or pancreatic insufficiency, gastroparesis, peptic ulcers, among others (4).

4. Untreated nutrient deficiencies

Untreated celiac disease causes intestinal damage in the body. Specifically this damage begins in the first part of the intestine (the duodenum) and can progress further from there. When the integrity of the gut is compromised, nutrients cannot be absorbed efficiently into the body which lead to deficiencies over time.

87% of people have one or more nutrient deficiencies upon diagnosis of celiac disease. 

The most common are: vitamin A, B6, B12 (8-41% of people newly diagnosed), folic acid (18-24%), iron (28-50%), vitamin D (20-66%) and/or zinc (54-67%) (5). Talk to your doctor or dietitian about being screened for nutrient deficiencies and how to correct them.

5. Relying on gluten free substitutes

Gluten free products can be a huge help when people are transitioning from a traditional way of eating to a gluten free lifestyle. Gluten free breads, buns, bagels, cakes, cookies, crackers and snacks are a major profitable section of the food market right now. Nutritionally? They do not usually have a lot of good stuff in there. Plus they are not very budget friendly!

Gluten free substitutes are usually higher in fat, sugar and lower in nutrients, whole grains and fibre. 

Instead of loading up on gluten free substitutes, considering simplifying your diet. Focus on whole, unprocessed foods and build your meals around those. Get back to the basics.

Vegetables and fruits

Whole grains and starchy vegetables like brown rice, quinoa, potatoes, sweet potatoes, corn, buckwheat, millet, etc.

Protein sources like beans, legumes, lentils, tofu, eggs, nuts, seeds, fish, chicken, meat, etc.

Calcium rich foods like milk, plant based beverages, yogurt, cheese, etc.

Natural flavours like oils, vinegars, herbs and spices

6. Unhappy gut bacteria

The amount and type of bacteria we have in our gut has a huge impact on our body and how we feel. Research in this area has exploded in the past ten years but there is so much we don’t yet know.

There is a theory that celiac disease can develop as a result of negative changes to gut microflora (bacteria in our gut).

It makes sense that we should focus on restoring that bacterial balance post diagnosis. How do we do this? One of the most important ways is to make sure we are getting enough FIBRE into our body.

Fibre feeds good bacteria in our gut. They in turn break it down to create something called “short chain fatty acids” which essentially is like expensive hand lotion for our gut cells. It’s soothing, calming and helps them grow and repair better.

Other ways to boost good bacteria is by consuming fermented and probiotic food products like yogurt, kimchi, sauerkraut, tempeh, miso, kombucha and kefir. Probiotic supplements can also help but they are not all created equal. Certain strains are proven to help different symptoms so speak to a health professional who knows the research behind them. Taking the wrong kind can make symptoms worse! (6)

celiac disease, persistent symptoms, IBS, registered dietitian, gluten intolerance

7. Trouble with dairy

Lactose is a type of carbohydrate (sugar) found in milk and dairy products. Normally the enzyme that is responsible for digesting or breaking down lactose in the intestine in found on the tips of the villi.

If the intestines are damaged, the process of digesting lactose will not work properly, if at all.

When that undigested milk sugar makes its way into large intestine, the bacteria in the gut have a party! They love sugar and eat it up very quickly and as a result produce a large amount of gas. This gas can contribute to bloating, cramping, diarrhea and pain some people experience.

It can be helpful to remove lactose for a few weeks at the beginning of the healing process to try to minimize symptoms. However some people actually regain the ability to digest lactose once the villi and intestinal lining heal. So don’t give up on lactose completely, it may just be a temporary issue.

There is some research that shows people with celiac disease are also commonly intolerant a certain protein in milk, specially casein. The study found that half of the participants showed inflammation to the gut in response to casein as well as gluten. For some people this can be a temporary intolerance and for others, it can be a long term issue.

8. IBS

Irritable bowel syndrome is defined as:

Recurrent abdominal pain or discomfort at least 3 days/month in the last 3 months associated with two or more of the following:

  • Improvement with defecation
  • Onset associated with a change in frequency of stool
  • Onset associated with a change in form (appearance) of stool

Research shows that 38-47% of people with celiac disease also have IBS. (6)

What can we do about it? There are a lot of products, supplements and treatments that promise to cure IBS related symptoms. The truth is that often they do not work. What works is removing dietary and lifestyle triggers. There are specific strategies around eating that can help. Research has validated a specific diet called the low FODMAP diet which is helpful for 70-75% of people experience symptom relief. This is meant to be an elimination diet in order to identify triggers and not a permanent diet. Work with a skilled dietitian to help manage your IBS related symptoms.

celiac disease, persistent symptoms, IBS, registered dietitian, gluten intolerance

Healing from celiac disease is a journey that’s not always straight forward. I fully understand this. Read more about our story here. As a dietitian, I can support you on your healing journey, help identify why persistent symptoms may be happening and address them with a nutrition focus.

I’m on a podcast! Hear me talk about persistent symptoms on A Canadian Celiac Podcast here.

Contact me or read more about how I can help.




  1. Sylvester, J.,A., Graff, L.,A., Rigaux, L,, Bernstein, C.,N., Leffler, D.,A, Kelly, C.,P., Walker, J.,R., Duerksen, D.,R.(2017). Symptoms of functional intestinal disorders are common in patients with celiac disease following transition to a gluten-free diet. Digestive Diseases and Sciences, 62(9): 2449-2454.
  2. Freeman, H. J. (2017). Dietary compliance in celiac disease. World Journal of Gastroenterology 23(15), 2635-2639. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5403742/
  3. Leonard, M., M., Sapone, A., Catassi, C., Fasano, F. (2017). Celiac Disease and Nonceliac Gluten Sensitivity:A Review. JAMA. 318(7):647-656.
  4. Leonard, A., Cureton, P., Fasano, A. (2017). Indications and use of the gluten contamination elimination diet for patients with non-responsive celiac disease. Nutrients, 9(1120).
  5. Wierdsma NJ et al. (2013). Vitamin and mineral deficiencies are highly prevalent in newly diagnosed celiac disease patients. Nutrients 5(10):3975-92.
  6. Piccolo, F., Francavilla, A., Polimeno, L., Semeraro, F., Cristofori, F., Castellaneta, S., Barone, M, Indrio, F., Gobbetti, M, De Angeli, M. (2018). Clinical and microbiological effect of a multispecies probiotic supplementation in celiac patients with persistent IBS-type symptoms: A randomized, Double-Blind, Placebo-controlled, Multicenter Trial. K Clin Gastroenterol  April [Epub ahead of print].

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