Celiac disease is diagnosed through a combination of blood tests and, in most cases, a small intestinal biopsy. The process typically starts with a screening blood test called tTG-IgA, which detects antibodies your immune system produces when it reacts to gluten. If that test is positive, an upper endoscopy with biopsies of the small intestine confirms the diagnosis by showing characteristic damage to the intestinal lining.
Getting an accurate diagnosis depends on one critical detail: you need to be eating gluten regularly when you’re tested. Going gluten-free before testing can cause both blood tests and biopsies to come back falsely normal.
Why You Must Be Eating Gluten Before Testing
The blood tests and biopsies used to diagnose celiac disease measure your body’s active immune response to gluten. If you’ve already cut gluten from your diet, that response quiets down, and your results may look normal even if you have the disease. This is one of the most common reasons for a missed diagnosis.
If you’ve already started a gluten-free diet before getting tested, you’ll need to do what’s called a gluten challenge. The standard approach is eating about 3 grams of gluten per day (roughly one and a half slices of bread) for at least 8 weeks before blood work. Some protocols call for higher amounts, around 8 to 10 grams daily (four to six slices of bread) for 6 to 8 weeks. If symptoms become severe during the challenge, your doctor may check antibody levels at the 2- to 4-week mark. A positive result at that point can move things along faster.
The First Step: Blood Tests
The initial screening test is the tissue transglutaminase IgA antibody test, known as tTG-IgA. It’s the preferred first-line test because it’s widely available and highly accurate, with a sensitivity between 78% and 100% and specificity between 90% and 100%. Your doctor should also order a total IgA level at the same time, because about 2 to 3% of people with celiac disease have IgA deficiency, a harmless immune quirk that makes IgA-based tests unreliable.
If your total IgA comes back low, your doctor will switch to IgG-based blood tests instead. These include IgG deamidated gliadin peptide (DGP) and IgG tTG tests, which don’t depend on your body’s IgA levels to work.
A second antibody test, the endomysial antibody (EMA-IgA) test, is sometimes used as a confirmatory step. It’s extremely specific, between 97% and 100%, meaning a positive result almost certainly indicates celiac disease. It’s more expensive and labor-intensive than tTG-IgA, so it’s typically reserved for cases where extra confirmation is helpful.
Some older tests are no longer recommended. Anti-gliadin antibody tests, intestinal permeability tests, and salivary or stool-based tests are not reliable enough for diagnosis and should be avoided.
Confirming With an Intestinal Biopsy
A positive blood test strongly suggests celiac disease, but for most adults the diagnosis is confirmed through an upper endoscopy with biopsies of the small intestine. During the procedure, a thin flexible tube is passed through your mouth to your duodenum (the first part of the small intestine), and small tissue samples are collected. The procedure itself usually takes about 15 to 20 minutes under light sedation.
Current guidelines call for at least six tissue samples: two from the duodenal bulb and four from the section just beyond it. Taking multiple samples matters because celiac damage can be patchy, appearing in some spots but not others. With this approach, sensitivity reaches up to 96%.
A pathologist examines the samples under a microscope and grades the damage using the Marsh classification system:
- Marsh 0: Normal tissue, no signs of celiac disease
- Marsh 1: Increased immune cells in the intestinal lining, but no structural damage
- Marsh 2: Increased immune cells plus elongated intestinal crypts (the valleys between the finger-like projections that absorb nutrients)
- Marsh 3a–3c: Immune cell increase, crypt changes, and varying degrees of villous atrophy, where the tiny finger-like projections that absorb nutrients become flattened or destroyed. This ranges from partial (3a) to subtotal (3b) to total flattening (3c)
Marsh 3 findings, combined with a positive blood test, are considered a definitive celiac diagnosis. Marsh 1 alone (increased immune cells without structural damage) is not enough to diagnose celiac disease on its own, since several other conditions can cause the same pattern.
Diagnosis in Children: When Biopsy Isn’t Required
Children can sometimes be diagnosed without a biopsy. European guidelines from ESPGHAN confirm that a biopsy-free diagnosis is safe when two conditions are met: the tTG-IgA level is at least 10 times the upper limit of normal, and a second blood sample comes back positive for endomysial antibodies (EMA-IgA). Both criteria must be present. This approach has been validated in large studies and is increasingly used in pediatric practice.
Children who have IgA deficiency and test positive on an IgG-based test still need a biopsy, since the no-biopsy pathway hasn’t been validated for that group. The same applies to children whose tTG-IgA levels are elevated but below the 10x threshold.
For adults, most gastroenterology guidelines still recommend biopsy confirmation. However, when an adult has very high tTG-IgA levels and a positive EMA on a second blood draw, some clinicians consider this a likely diagnosis, particularly for patients who are unwilling or unable to undergo endoscopy.
The Role of Genetic Testing
Genetic testing for celiac disease looks at two gene variants called HLA-DQ2 and HLA-DQ8. About 95% of people with celiac disease carry one or both of these markers. However, roughly 30 to 40% of the general population carries them too, so a positive genetic test doesn’t mean you have celiac disease. It only means it’s possible.
The real power of genetic testing is in ruling the disease out. If you don’t carry either HLA-DQ2 or HLA-DQ8, your chances of having celiac disease are extremely low. This makes the test most useful in specific situations: when someone has already gone gluten-free before being tested and doesn’t want to do a full gluten challenge, when biopsy results are unclear, or when screening family members to determine who needs ongoing monitoring. Genetic testing is not recommended as a first step in diagnosis.
What Happens After Diagnosis
Once celiac disease is confirmed, a strict gluten-free diet is the treatment. Your doctor will typically recheck your tTG-IgA levels periodically to make sure they’re trending downward, which indicates your immune system is calming and your intestine is healing. In a large study of children with celiac disease, about 67% had normal antibody levels within 12 months of starting a gluten-free diet, rising to 90% by 24 months. The median time to normalization was 9 months.
If your antibody levels were very high at diagnosis, it can take longer for them to come down, sometimes 24 to 36 months. Guidelines generally recommend further investigation if antibodies remain elevated after 12 months, since persistent elevation can signal ongoing gluten exposure, whether intentional or accidental through cross-contamination.
Your doctor may also recommend a follow-up biopsy one to two years after starting the diet to confirm that the intestinal lining has healed, though practices vary on this point. Nutritional testing for iron, vitamin D, calcium, and B12 deficiencies is common at diagnosis and during follow-up, since these are frequently low in people with untreated celiac disease.