Celiac disease is an autoimmune condition in which eating gluten triggers your immune system to attack the lining of your small intestine. It affects roughly 1% of the population, though up to 83% of people who have it in the United States remain undiagnosed or misdiagnosed. The damage it causes interferes with nutrient absorption and can produce a wide range of symptoms, from digestive problems to joint pain, skin rashes, and bone loss.
How Gluten Triggers Intestinal Damage
Gluten is a protein found in wheat, rye, and barley. Most people digest it without issue, but in celiac disease, the immune system treats gluten fragments as a threat. The process starts when gluten reaches the small intestine and causes the gut lining to become more permeable than normal. A protein called zonulin loosens the tight seals between intestinal cells, allowing partially digested gluten fragments to slip through into the tissue underneath.
Once there, an enzyme modifies these gluten fragments in a way that makes them highly visible to the immune system. Immune cells recognize the modified gluten, lock onto it, and launch an inflammatory response. This inflammation does two things: it recruits more immune cells that directly kill the cells lining the intestine, and it floods the area with inflammatory signals that sustain the attack as long as gluten keeps arriving.
Over time, this cycle flattens the tiny finger-like projections called villi that line the small intestine. Villi are what give the intestine its enormous surface area for absorbing nutrients. When they’re destroyed, that surface area shrinks dramatically, leading to malabsorption of vitamins, minerals, and calories. This is the root cause of most celiac symptoms, whether they show up in the gut or elsewhere in the body.
Who Is at Risk
Celiac disease requires a specific genetic setup. About 90% of people with celiac carry a gene variant called HLA-DQ2, and most of the remaining 5 to 10% carry HLA-DQ8. Without one of these gene variants, celiac disease essentially cannot develop. However, these genes are common in the general population, and most people who carry them never develop the disease. The genes are necessary but not sufficient on their own.
Risk varies by the specific combination of gene variants a person inherits. People who are homozygous for DQ2.5 (meaning they got the variant from both parents) have the highest risk, greater than 1 in 10. Those with a single copy of DQ8 have a lower but still elevated risk, around 1 in 100. Environmental factors, including the timing and amount of gluten introduction in infancy, gut infections, and other stressors, appear to play a role in whether the disease actually activates in someone who is genetically susceptible.
Celiac disease also clusters with other autoimmune conditions. People with type 1 diabetes, autoimmune thyroid disease (Hashimoto’s), and adrenal autoimmunity share overlapping genetic risk factors. In one Swedish study of over 5,000 children with type 1 diabetes, nearly 10% also had biopsy-confirmed celiac disease. About one-third of adults newly diagnosed with celiac disease already have antibodies associated with at least one other autoimmune condition.
Symptoms in Adults and Children
Celiac disease is sometimes divided into “classical” and “non-classical” forms, but in practice the symptoms overlap and vary enormously from person to person. Classical celiac disease looks like a straightforward malabsorption problem: chronic diarrhea, pale or fatty stools, weight loss, and in children, failure to thrive or delayed growth. This is the presentation most people picture, but it’s not the most common one.
Non-classical celiac disease is more subtle and often the reason for delayed diagnosis. Adults frequently present with iron-deficiency anemia that doesn’t respond to supplements, chronic fatigue, brain fog, migraines, joint pain, or tingling and numbness in the hands and feet (peripheral neuropathy). Some people develop dermatitis herpetiformis, an intensely itchy, blistering skin rash that is so specific to celiac disease it’s sometimes called “celiac of the skin.” Others have unexplained elevated liver enzymes, recurrent mouth ulcers, missed periods, or early bone loss.
Children can show irritability, attention and learning difficulties, anxiety, damaged tooth enamel, short stature, or delayed puberty, sometimes with minimal digestive complaints. A subset of people have what’s called silent celiac disease: intestinal damage visible on biopsy but no noticeable symptoms at all. These cases are typically found through screening of family members or people with associated autoimmune conditions.
How Celiac Disease Is Diagnosed
Diagnosis typically involves two steps: a blood test followed by an intestinal biopsy. The key requirement is that you must still be eating gluten for the tests to work. Going gluten-free before testing can cause both blood tests and biopsies to come back falsely normal.
The first-line blood test measures antibodies against tissue transglutaminase (tTG-IgA). It has a sensitivity between 78% and 100% and a specificity between 90% and 100%, making it a strong screening tool. If that test is positive, a second antibody test (EMA-IgA) may be ordered to increase diagnostic certainty, with specificity reaching 97% to 100%. For children under two, additional antibody tests may be added because the standard tests can be less reliable at that age.
If blood tests suggest celiac disease, the next step is an upper endoscopy with biopsies taken from the duodenum (the first section of the small intestine). A doctor passes a thin, flexible tube through the mouth and into the small intestine to collect small tissue samples, which are then examined under a microscope for the characteristic pattern of flattened villi, increased immune cells, and overgrowth of the intestinal crypts. This biopsy remains the gold standard for confirming the diagnosis in adults.
There is one exception: when the initial tTG-IgA result is extremely high (more than 10 times the upper limit of normal) and a follow-up EMA-IgA test is also positive, some guidelines allow diagnosis without biopsy. This approach is more widely accepted for children than adults.
What Happens Without Treatment
Left untreated, celiac disease causes ongoing intestinal damage and progressively worsening malabsorption. The most common nutritional consequences are iron deficiency, low vitamin D, low calcium, and deficiencies in folate and vitamin B12. Over years, calcium and vitamin D malabsorption leads to weakened bones, increasing the risk of osteoporosis and fractures.
People with untreated celiac disease also have a slightly increased risk of certain cancers, particularly small bowel lymphoma and small bowel cancer. This risk was once thought to be quite high, but more recent research shows it is smaller than previously estimated, and it returns to the general population’s baseline risk after a sustained gluten-free diet. Poorly controlled celiac disease during pregnancy is associated with a higher chance of having a low birth weight baby.
Living on a Gluten-Free Diet
A strict, lifelong gluten-free diet is currently the only established treatment. This means eliminating all foods containing wheat, rye, and barley, including less obvious sources like soy sauce, beer, some salad dressings, and many processed foods that use wheat-based thickeners or fillers.
In the United States, the FDA requires any food labeled “gluten-free” to contain less than 20 parts per million (ppm) of gluten. This threshold represents the lowest level that can be reliably measured with current testing methods. Foods cannot carry a gluten-free label if they contain any ingredient derived from wheat, rye, or barley that has not been processed to remove gluten below that 20 ppm limit.
Cross-contamination is a real concern. Shared toasters, cutting boards, cooking oil, and even airborne flour in a kitchen can introduce enough gluten to sustain intestinal damage. Many people with celiac disease find they need dedicated cookware and careful restaurant communication to stay safe. Even small, repeated exposures below the level that causes noticeable symptoms can prevent the intestine from healing.
For most people, the intestinal lining begins to recover within weeks of removing gluten, though full healing can take months to two years depending on the extent of damage. Symptoms like fatigue, brain fog, and digestive problems often improve within the first few weeks. Bone density gradually improves with restored absorption of calcium and vitamin D, though some people need supplementation to correct existing deficiencies.
Prevalence and the Diagnosis Gap
Celiac disease affects an estimated 1 in 133 Americans. Screening studies in Europe suggest the true prevalence may be even higher: mass screening of Italian children found a rate of 1.6%, and estimates in Finland reach nearly 2%. Global incidence is increasing significantly, a trend that appears to reflect genuine rises in the disease rather than just improved detection.
Despite this, the majority of people with celiac disease don’t know they have it. The 83% undiagnosed figure in the U.S. is partly because the condition mimics so many other things. People spend an average of six to ten years bouncing between diagnoses of irritable bowel syndrome, chronic fatigue, anxiety, or anemia before celiac disease is identified. The non-classical presentation, where gut symptoms are mild or absent, is a major driver of this delay.