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Ask the Science Team: Why do I continue to have symptoms on the gluten-free diet?

January 21, 2022


There are reports of comorbid conditions (like migraines for instance) and how a higher percentage of people with celiac disease have said comorbidities. Is that true even for people who are diagnosed and strictly gluten-free? Why do I continue to have symptoms like this even on the gluten-free diet?

Answer from the Beyond Celiac Science Team:

Symptoms of celiac disease often continue in patients who follow the gluten-free diet. Studies have shown that people with celiac disease on the gluten-free diet continue to have symptoms, elevated antibodies to gluten detected in blood tests, and damage to the nutrient-absorbing lining of the intestine.


The role of the gluten-free diet is often considered in studies, and researchers will look at whether study participants are following the diet. For example in this study about headaches, investigators noted that headaches are more common in those who have celiac disease, but the gluten-free diet is often an effective treatment. Up to 75 percent of adult patients with celiac disease reported their headaches ended when they followed the diet. In children with celiac disease, headaches resolved in 71 percent. The authors note this is consistent with improvement in neuropathy pain. 

While the majority of people found that their headaches ended when they followed the diet, that was not the case for 25 percent. For those study participants, headaches continued despite the gluten-free diet. 

Brain Changes

In this study that looked at brain images, researchers from the University of Sheffield, Sheffield, UK, attributed neurological damage seen in brain scans to gluten exposure, including inadvertent exposure in those following the gluten-free diet. This means that in this study, those who are following a gluten-free diet that only included inadvertent exposure still had changes in the brain. Most celiac disease experts agree that it is nearly impossible to maintain a diet that is 100 percent free of gluten despite best efforts to do so. 

Beyond Celiac has awarded a two-year established investigator grant to the Sheffield researchers to expand investigation of the neurological and neuropsychological manifestations of celiac disease and gluten-related disorders. 

The new research will examine the relationship between findings from brain scans of patients with gluten-related disorders and a variety of different parameters. The study will focus on how effectively the gluten-free diet treats these neurological problems and will further investigate long-term effects on cognitive function, severity of depression and anxiety symptoms, and overall quality of life. This study is designed to answer questions about the role and impact of the diet in terms of neurological symptoms. 

Non-Responsive Celiac Disease

Neurological symptoms are not the only ones that sometimes continue after a person has been diagnosed with celiac disease and goes on a gluten-free diet. 

Non-responsive celiac disease, which is defined as persistent symptoms, signs or abnormalities typical of the condition despite 6 to 12 months of strict adherence to a gluten-free diet, affects up to 30 percent of patients, according to a 2020 study. 34 to 64 percent of celiac disease patients have intestinal healing two years after diagnosis, the study says, increasing to 66 to 85 percent in five years. However, some patients never achieve complete resolution of intestinal inflammation, according to the study.

A 2017 study by researchers at the University of Chicago Celiac Center found that even after more than two years on the gluten-free diet about 60 percent of children and adults have ongoing non-gastrointestinal symptoms. Short stature, fatigue and headache were most common in children, while iron deficiency anemia, fatigue, headaches and psychiatric symptoms were most common in adults.

A 2016 study of children with celiac disease found one in five may not heal despite following the gluten-free diet for at least a year. The children, who were seen between 2008 and 2015, also had a follow-up biopsy at least 12 months after starting a gluten-free diet. The study found that 19 percent had persistent intestinal damage when the second biopsy was done.

A newly published study by researchers in Rome found that about one-third of people with celiac disease on the gluten-free diet had persistent symptoms or signs of malabsorption at the point when a follow-up biopsy was done. People with celiac disease who seem to be doing well on a gluten-free diet may have ongoing, low-level intestinal inflammation, according to another new study that looked at complete protein profiles in biopsy samples. Study authors said their findings raise the question of whether the standard gluten-free diet is sufficient to stop the immune reaction that occurs in celiac disease.


Many studies do distinguish between those with celiac disease who follow the gluten-free diet and those who are diagnosed but do not follow the gluten-free diet. In some studies, only those who follow a gluten-free diet can participate in the study. Research news posts on the Beyond Celiac website do note the details about study participants, including whether they are on the gluten-free diet. Often in a clinical trial, study participants must be on a gluten-free diet for some period of time, and many of these only include patients who continue to have symptoms.

Overall, scientific evidence shows that the gluten-free diet is not a complete treatment for celiac disease because those who follow it may continue to have symptoms or to have intestinal damage that is revealed by a follow-up biopsy. That evidence is behind the Beyond Celiac commitment to find new treatments and a cure by 2030. 


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