Celiac disease is a chronic autoimmune condition where eating gluten triggers your immune system to attack the lining of your small intestine. It affects roughly 1% of people in Western countries, though a large proportion of cases remain undiagnosed. The damage it causes can interfere with nutrient absorption and produce symptoms that range far beyond digestive trouble.
What Happens Inside Your Body
When someone with celiac disease eats gluten, a protein found in wheat, barley, and rye, the process starts at the gut wall. Gluten fragments cause cells lining the intestine to release a protein called zonulin, which loosens the tight seals between those cells. This makes the intestinal wall more permeable, allowing partially digested gluten to slip through into the tissue underneath.
Once there, an enzyme called tissue transglutaminase chemically modifies the gluten fragments, making them more visible to the immune system. Immune cells then mount two simultaneous attacks. One involves specialized T cells that directly kill the cells lining the intestine. The other triggers widespread inflammation through signaling molecules that recruit even more immune activity to the area. Over time, this repeated assault flattens the tiny, finger-like projections (villi) that line the small intestine and are responsible for absorbing nutrients from food. That flattening, called villous atrophy, is the hallmark damage of celiac disease.
Genetics and Risk
Celiac disease has a strong genetic component. About 90% of people with celiac disease carry a specific immune gene variant called HLA-DQ2, and most of the rest carry a related variant called HLA-DQ8. Together, these genes are present in roughly 98% of celiac patients. But carrying the gene doesn’t mean you’ll develop the disease. Around half the general population carries one of these variants, yet only a small fraction ever develops celiac disease. Other genetic and environmental factors, some still being identified, determine who actually gets sick.
First-degree relatives of someone with celiac disease have a significantly higher risk. If a parent, sibling, or child has it, genetic testing for HLA-DQ2 and DQ8 can be a useful first step. A negative result essentially rules out celiac disease, since the condition almost never develops without one of these gene variants.
Symptoms Beyond the Gut
The “classic” presentation of celiac disease involves diarrhea, bloating, abdominal pain, and weight loss. But many people, especially adults, present with symptoms that seem to have nothing to do with digestion. This is one reason celiac disease goes undiagnosed so often.
Iron-deficiency anemia that doesn’t respond to supplements is one of the most common non-digestive signs. Because the damaged intestine can’t absorb iron, calcium, vitamin D, and B vitamins properly, a cascade of deficiency-related problems can develop: bone thinning (osteoporosis), fatigue, muscle pain, and easy bruising. Women may experience missed periods, difficulty getting pregnant, recurrent miscarriage, or early menopause.
Neurological symptoms are more common than most people realize. These include migraines, peripheral neuropathy (tingling, numbness, or burning in the hands and feet), balance problems known as gluten ataxia, and what many patients describe as “brain fog,” a cluster of symptoms including difficulty concentrating, short-term memory lapses, and confusion after gluten exposure. Anxiety and depression also occur at higher rates.
The skin condition most closely tied to celiac disease is dermatitis herpetiformis, an intensely itchy rash of small blisters that typically appears on the elbows, knees, and buttocks. Other skin-related associations include patches of hair loss (alopecia areata), chronic hives, and psoriasis.
How Celiac Disease Is Diagnosed
The first-line screening test measures antibodies to tissue transglutaminase (tTG-IgA) in a blood sample, along with total IgA levels. If tTG-IgA is elevated, the traditional next step is an upper endoscopy with biopsies of the small intestine to look for villous atrophy. This combination of positive blood work and biopsy findings has been the gold standard for decades.
For children, updated European guidelines now allow a diagnosis without biopsy in certain cases. If the tTG-IgA level is more than 10 times the upper limit of normal and a second confirmatory antibody test (anti-endomysial antibodies) is also positive, the diagnosis can be made on blood work alone. Some adult gastroenterologists are beginning to adopt a similar approach, though biopsy remains more standard in adults.
One critical point: you need to be eating gluten regularly for the tests to work. If you’ve already removed gluten from your diet before being tested, both the antibody levels and biopsy results can come back falsely normal. If you suspect celiac disease, get tested before going gluten-free.
Living on a Gluten-Free Diet
A strict, lifelong gluten-free diet is currently the only treatment. This means eliminating all wheat, barley, rye, and any products derived from them. For most people, the intestinal lining begins to heal within weeks to months, though full recovery can take a year or longer in adults.
Foods labeled “gluten-free” in the United States must contain less than 20 parts per million (ppm) of gluten, a threshold set by the FDA and used internationally. This is the lowest level that can be reliably measured with current testing methods, and most people with celiac disease tolerate foods at or below this level without symptoms or intestinal damage.
The challenge goes well beyond avoiding bread and pasta. Gluten hides in soy sauce, salad dressings, marinades, processed meats, beer, and many packaged foods where wheat-based ingredients serve as thickeners or stabilizers. Oats are naturally gluten-free but are frequently contaminated during processing, so only oats specifically labeled gluten-free are considered safe. Cross-contamination in shared kitchens, from a common toaster or cutting board, can also be enough to cause a reaction.
Non-food products occasionally cause problems too. Lipstick and lip balm can contain gluten-based ingredients that get swallowed incidentally. Some toothpastes and mouthwashes also contain gluten. While gluten in a hand lotion won’t cause intestinal damage (it has to be ingested), anything that touches your lips or mouth is worth checking. When in doubt, contacting the manufacturer directly is the most reliable way to confirm a product’s status.
Nutritional Deficiencies and Long-Term Risks
Because celiac disease impairs absorption in the small intestine, nutritional deficiencies are common at diagnosis and sometimes persist even after starting a gluten-free diet. The most frequent are iron, calcium, vitamin D, folate, vitamin B12, and zinc. These deficiencies explain many of the symptoms people experience, from anemia and bone loss to skin rashes caused by zinc or niacin depletion. Most doctors will check nutrient levels at diagnosis and monitor them during follow-up, often recommending supplements until the gut has healed enough to absorb normally.
Untreated celiac disease is also associated with a higher risk of developing other autoimmune conditions, including type 1 diabetes, autoimmune thyroid disease, and autoimmune liver disease. The relationship appears to run in both directions: people with these conditions are more likely to have celiac disease, and people with undiagnosed celiac disease are more likely to develop them over time. There is also a small but real increased risk of certain cancers, particularly a type of intestinal lymphoma, in people whose celiac disease remains untreated or poorly controlled for many years.
When the Diet Doesn’t Work
Most people improve significantly on a strict gluten-free diet, but a small number continue to have symptoms and ongoing intestinal damage. The most common reason is unintentional gluten exposure, which is worth investigating thoroughly before assuming something else is wrong. Working with a dietitian who specializes in celiac disease can help identify hidden sources of contamination.
For the roughly 10% to 18% of patients evaluated at referral centers whose symptoms persist despite genuinely strict adherence, the diagnosis of refractory celiac disease may apply. This is defined as continued villous atrophy and malabsorptive symptoms after at least 6 to 12 months on a gluten-free diet, once other causes have been ruled out. Refractory celiac disease is rare but serious, and it requires specialized management beyond dietary changes alone.