Why Many Kids with Celiac Disease Still Have Stomach Pain—Even on a Gluten-Free Diet

Celiac.com 12/17/2025 - This study explores why many children with celiac disease continue to experience stomach discomfort and other digestive symptoms even after following a strict gluten-free diet. Researchers focused on a group of conditions known as “disorders of gut–brain interaction,” which affect how the digestive system and nervous system communicate. These conditions are not caused by visible damage to the intestines but by complex changes in how the brain and gut send signals to each other.

The findings reveal that these gut–brain interaction disorders are surprisingly common among children with celiac disease, even when their blood tests show improvement and they are successfully avoiding gluten. This discovery could reshape how doctors understand and treat ongoing digestive problems in young patients with celiac disease.

Background: When Gluten Is Not the Whole Story

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Celiac disease is an autoimmune condition that causes the immune system to attack the small intestine when gluten is consumed. The standard treatment is a lifelong gluten-free diet, which usually leads to healing of the intestine and relief of symptoms. However, many children and adults continue to have abdominal pain, constipation, or nausea even after following the diet carefully. This ongoing discomfort has puzzled doctors and families for years.

Disorders of gut–brain interaction, previously known as “functional gastrointestinal disorders,” offer a possible explanation. In these conditions, the digestive system looks normal under medical tests, but the nerves and muscles that control digestion are overly sensitive or miscommunicate with the brain. Examples include functional abdominal pain, constipation, and irritable bowel–type symptoms. In adults with celiac disease, these overlapping disorders are known to occur frequently, but little was known about how often they affect children in the United States—until now.

Study Design and Participants

The researchers reviewed medical records from 191 children and young adults between the ages of 4 and 21 who had biopsy-confirmed celiac disease. To be included, all participants had to meet three key criteria:

• They were following a gluten-free diet as prescribed.
• Their blood tests showed a clear decline in antibodies (a marker that gluten exposure and inflammation were improving).
• They had at least one follow-up visit with a pediatric gastroenterologist between 9 and 24 months after diagnosis.

During these visits, doctors assessed whether the children continued to experience digestive symptoms and whether those symptoms met the internationally recognized Rome IV criteria for disorders of gut–brain interaction. The researchers also looked at other health conditions and symptoms that might predict who was more likely to develop these disorders.

Key Findings

The results were striking: nearly half—43 percent—of the children who were strictly following a gluten-free diet met the diagnostic criteria for at least one gut–brain interaction disorder. This means that almost one in two children with celiac disease may continue to have stomach-related symptoms that cannot be explained by gluten exposure or intestinal damage alone.

Among the children diagnosed with these disorders, two were especially common:

• Functional constipation – 33 percent of affected children experienced chronic difficulty passing stool without any structural or biochemical reason.
• Functional abdominal pain – 29 percent had ongoing stomach pain even though their intestines had healed and gluten antibodies were decreasing.

Other less frequent but notable symptoms included nausea, vomiting, and generalized abdominal discomfort.

Risk Factors and Predictive Clues

The study also identified several patterns that could help predict which children are most likely to experience these overlapping conditions. Children who had abdominal pain, constipation, or vomiting when they were first diagnosed with celiac disease were more likely to develop a disorder of gut–brain interaction later on—even after their intestinal health improved on a gluten-free diet.

In addition, some non-digestive symptoms were linked to an increased risk. Children with joint hypermobility (unusually flexible joints), frequent headaches, or chronic musculoskeletal pain were more likely to experience these gut–brain conditions. These findings suggest that the problem may not lie in the digestive tract alone but could involve how the nervous system processes pain and sensation throughout the body.

Why the Gut and Brain Connection Matters

The gut and brain are closely connected through a network of nerves, hormones, and chemical signals often referred to as the “gut–brain axis.” In disorders of gut–brain interaction, this communication system becomes unbalanced, causing the gut to overreact to normal sensations like stretching, digestion, or stress. The result is real, distressing symptoms—pain, bloating, or irregular bowel movements—even when the digestive system appears normal under medical testing.

For children with celiac disease, this can mean that their ongoing discomfort is not due to accidental gluten exposure or incomplete healing but rather to lingering nerve sensitivity or altered brain–gut communication. Understanding this connection is crucial, because it changes how doctors approach treatment. Instead of assuming gluten is still the problem, clinicians can look at the bigger picture and consider therapies that target nerve regulation, stress reduction, and brain–gut balance.

Clinical Implications

The study emphasizes the need for healthcare providers to be aware that children with celiac disease can develop disorders of gut–brain interaction even when they are doing everything right. A strict gluten-free diet may not be enough to eliminate all symptoms. Recognizing the signs early allows for appropriate management that could include dietary adjustments beyond gluten elimination, psychological support, or medications that regulate gut function and nerve signaling.

The researchers recommend that pediatricians and gastroenterologists maintain a “high index of suspicion” for these disorders, especially when a child continues to have stomach pain or bowel problems despite clear improvement in gluten antibody levels. Early identification could help reduce unnecessary anxiety and testing for both families and patients while improving quality of life.

What This Means for Families and Patients

For parents of children with celiac disease, it can be frustrating when symptoms persist despite careful gluten avoidance. This study offers an important message: persistent symptoms do not always mean the child is being exposed to gluten. In many cases, the issue may lie in how the gut and brain communicate after the intestinal injury from celiac disease has healed.

Understanding this helps families take a more compassionate and informed approach. It means that the child’s ongoing discomfort is not “in their head” or due to noncompliance but is part of a complex neurological and digestive process that can be managed with the right tools. Treatment might include a combination of dietary counseling, stress-reduction techniques, and medical or behavioral therapies focused on the gut–brain connection.

Conclusion

This study reveals that nearly half of children with celiac disease continue to experience digestive symptoms related to disorders of gut–brain interaction, even while adhering strictly to a gluten-free diet. Functional constipation and abdominal pain are the most common issues, and symptoms at diagnosis—such as abdominal discomfort, constipation, and vomiting—may predict who is most at risk later.

For people living with celiac disease, these findings highlight an essential truth: healing the intestine is only one part of recovery. The nervous system’s ongoing role in gut function means that lasting symptom relief may require attention to both diet and the gut–brain connection. Recognizing and treating these overlapping conditions can lead to better overall health, fewer frustrations, and a clearer path to wellness for children and families managing celiac disease.

Read more at: onlinelibrary.wiley.com