Human body · Digestion

Inside Celiac Disease

Your small intestine is lined with tiny finger-like villi that soak up the nutrients from your food. In celiac disease, eating gluten makes the body's own immune system wear them down. Turn the model, drag the slider, and watch it happen.

Interactive model of the small-intestine lining

Your browser couldn't start the 3D view. Every stage is described in words on this page, just below the model.

When the view is focused, use the arrow keys to turn it and the plus and minus keys to zoom.

Slide from a healthy gut to the most severe damage.

Drag to turn, scroll or pinch to zoom. Keyboard: focus the model, then use the arrow keys and plus or minus.

Where the model is in the body A simple outline of the esophagus, stomach and small intestine, with the duodenum, the C-shaped first part of the small intestine just after the stomach, highlighted.
You are here: the duodenum, the first part of the small intestine, just after the stomach. Celiac damage is usually most severe in this first stretch,10 and it's where doctors take the biopsy samples that confirm the disease.2
Marsh 0

Healthy lining

  • Villi and gut lining
  • Immune cells (lymphocytes) in the lining
  • Nutrients from digested food

A simplified illustration, not to scale. The stages follow the Modified Marsh scale doctors use to grade a biopsy.2

What am I looking at?

A short section of the duodenum, the first part of the small intestine, sliced along its length. The bottom half of the tube is solid so you can see inside it; the top half is drawn as faint glass, and fades away as you zoom in. The pink fingers lining the inside wall are villi. The near end is cut open like a slice of cake, showing the layers of the wall: the narrow pockets just under the surface are crypts, where new lining cells are made, and the darker band at the bottom is muscle. Purple dots are immune cells sitting in the lining. Gold specks are nutrients from digested food flowing down the tube.

In a healthy gut, the nutrients brush against all that villus surface and get absorbed. Move the slider and the villi shrink and flatten, the crypts deepen, immune cells crowd in, and more of the nutrients flow straight past. "Play the healing" shows what a strict gluten-free diet allows: the villi can grow back over time. "See how it's diagnosed" sends an endoscope down the tube to take a sample, then shows that sample under a microscope at whichever stage the slider is set to.

The model is an illustration of what a pathologist sees under the microscope, not a picture of any one person's gut.

What the villi do

The lining of the small intestine is covered in villi: small, finger-like projections that absorb nutrients from food.13 Thanks to all that folding, the inner surface of the small intestine covers about 30 square meters, roughly the floor of a small studio apartment, packed inside your belly.8

That surface is the point. The more of it there is, the more iron, vitamins and other nutrients the body can take in. When the villi are damaged, they can't properly absorb iron, vitamins and other nutrients.4

What happens in celiac disease

Celiac disease is a serious autoimmune disease. In people who are genetically predisposed, eating gluten, a protein found in wheat, rye and barley, leads to damage in the small intestine: the immune system attacks the lining and damages the villi.1

It doesn't take much. Even small amounts of gluten, such as crumbs from a cutting board or toaster, can trigger intestinal damage.1

Genes set the stage. Almost everyone with celiac disease carries a gene variant called HLA-DQ2 or HLA-DQ8. About 30 to 40 percent of all people carry one of them, but only about 3 percent of those carriers develop the disease.9 It runs in families: a parent, child or sibling of someone with celiac disease has a 1 in 10 risk, and it can develop at any age once a person starts eating gluten.1

It isn't only a stomach problem. More than half of adults with celiac disease have symptoms outside the digestive system, such as iron-deficiency anemia, weakened bones, an itchy skin rash, mouth ulcers, headaches, nerve problems and joint pain.3

The stages, one by one

When a pathologist looks at a biopsy under the microscope, they grade the damage on the Modified Marsh scale.2 These are the same stages as the slider in the model.

    By the numbers

    • 1 in 100people worldwide are estimated to have celiac disease.1
    • About 30%of them are properly diagnosed.1
    • 1 in 10risk for a parent, child or sibling of someone with it.1
    • 1.4% and 0.7%of people worldwide, by blood test and by biopsy, in a review of 96 studies.7

    How it's diagnosed

    It usually starts with a blood test for antibodies, such as tissue transglutaminase antibodies.4 If the tests point to celiac disease, a doctor confirms it with an endoscopy: a thin, flexible scope passes through the mouth into the small intestine and takes several tiny tissue samples from the duodenum. The Celiac Disease Foundation calls this biopsy the gold standard, and recommends at least 4 to 6 samples. A pathologist then examines them under a microscope and grades them on the Modified Marsh scale, the stages in the model above.2

    Don't go gluten-free before you're tested. Starting the diet first affects the test results, so the disease can be missed.4

    Can the gut heal?

    Yes, often, but it takes time. Celiac disease can't be cured,4 and the only treatment is lifelong adherence to a strict gluten-free diet,1 which lets symptoms settle and the villi heal.4

    • Children usually heal fastest. The American College of Gastroenterology's guideline reports healing in 95 percent of children within two years of starting the diet.5
    • Adults take longer. The same guideline cites a US study in which the median time to heal was 3 years.5 In a Mayo Clinic study of 241 adults, the lining had recovered in 34 percent after two years and 66 percent after five, so about a third still had damage at five years.6
    • Rarely, the damage doesn't respond to a strict gluten-free diet at all. This is called refractory celiac disease.3

    Why it matters over a lifetime

    Celiac disease is sometimes treated as a food fad. The research says otherwise. When it goes undiagnosed, or the diet isn't followed, years of damage and poor absorption can lead to:

    • Malnutrition and anemia, because the damaged villi can't take in enough iron, vitamins and other nutrients.34
    • Weak bones: bone thinning (osteoporosis) and fractures.34
    • Fertility problems and miscarriage.34
    • Nerve problems, including seizures and nerve damage in the hands and feet.3
    • Other autoimmune diseases, such as type 1 diabetes and autoimmune thyroid disease.1
    • Certain cancers: a higher risk of intestinal lymphoma and small bowel cancer.3 The Celiac Disease Foundation puts the risk of small bowel cancers at 4 times higher, and of coronary artery disease at 2 times higher, for people with celiac disease.1

    Timing matters. In a 1999 study cited by the Celiac Disease Foundation, the later celiac disease was diagnosed, the more likely a person was to also have another autoimmune condition: 10.5 percent when diagnosed at ages 2 to 4, rising to 34 percent when diagnosed after age 20.1

    This page explains the science in general terms. It isn't medical advice. If you think you or someone you love might have celiac disease, talk to a doctor.

    Keep exploring

    • Quiz · 24 questions

      Inside Celiac Disease Quiz

      Twenty-four questions on everything above. Score 18 or more to earn a certificate.

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      Spot the Gluten

      Cornflakes, shampoo, play dough, soy sauce: which could expose someone with celiac disease to gluten? Some answers surprise people.

    • Daily life · with a cost calculator

      Living With Celiac Disease: The Hidden Costs

      What a strict gluten-free life really costs in money, time, eating out and peace of mind.

    Sources

    1. Celiac Disease Foundation. What is celiac disease?
    2. Celiac Disease Foundation. Diagnosis (endoscopy, biopsy and the Modified Marsh scale).
    3. Mayo Clinic. Celiac disease: Symptoms and causes.
    4. MedlinePlus, U.S. National Library of Medicine. Celiac disease – sprue.
    5. Rubio-Tapia A, Hill ID, Kelly CP, Calderwood AH, Murray JA. ACG Clinical Guidelines: Diagnosis and Management of Celiac Disease. American Journal of Gastroenterology, 2013. PubMed 23609613. (An updated guideline was published in 2023.)
    6. Rubio-Tapia A, Rahim MW, See JA, Lahr BD, Wu TT, Murray JA. Mucosal recovery and mortality in adults with celiac disease after treatment with a gluten-free diet. American Journal of Gastroenterology, 2010. PubMed 20145607.
    7. Singh P, Arora A, Strand TA, et al. Global prevalence of celiac disease: systematic review and meta-analysis. Clinical Gastroenterology and Hepatology, 2018. PubMed 29551598.
    8. Helander HF, Fändriks L. Surface area of the digestive tract – revisited. Scandinavian Journal of Gastroenterology, 2014. PubMed 24694282.
    9. Celiac Center, Beth Israel Deaconess Medical Center. Genetics (gene testing) (PDF).
    10. GPnotebook. Coeliac disease: pathology (the changes are most severe at the start of the small intestine and less marked further along).

    Accessibility

    This page was built to be accessible: it works from the keyboard, it is built for screen readers, and the 3D model has text alternatives. Every stage shown in the model is also described in words above. It has been checked with automated accessibility tools, but it has not had a formal accessibility audit.