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The only way to confirm a celiac disease diagnosis is to have an intestinal biopsy. A pathologist will assign a Modified Marsh Type to the biopsy findings. A Type of 3 indicates symptomatic celiac disease. However, Types 1 and 2 may also indicate celiac disease.

Why an Intestinal Biopsy?


An intestinal (duodenal) biopsy is considered the “gold standard” for diagnosis because it will tell you (1) if you have celiac disease, (2) if your symptoms improve on a gluten-free diet due to a placebo effect (you feel better because you think you should) or (3) if you have a different gastrointestinal disorder or sensitivity which responds to change in your diet.

If the results of the antibody or genetic screening tests are positive, your doctor may suggest an endoscopic biopsy of your small intestine. An endoscopy is a procedure that allows your physician to see what is going on inside your GI tract. A scope is inserted through the mouth and down the esophagus, stomach and small intestine, giving the physician a clear view and the option of taking a sample of the tissue.

This is usually an outpatient procedure. Samples of the lining of the small intestine will be studied under a microscope to look for damage and inflammation due to celiac disease. It is recommended that the doctor take at least 4-6 duodenal samples from the second part of duodenum and the duodenal bulb, in order to obtain an accurate diagnosis.

IMPORTANT: If you are currently on a gluten-free diet, your physician may recommend a gluten challenge to allow antibodies to build in your bloodstream prior to testing. Recommendations range from eating 1/2 slice of bread or a cracker daily for 12 weeks to eating 3 grams of gluten for 2 weeks. A gluten challenge should only be supervised by a physician trained in celiac disease, who can move you immediately to a biopsy if your symptoms are severe. Never undertake a gluten challenge when pregnant.

What Does the Intestinal Biopsy Show? (Give Me the Science)

  • Density of intra-epithelial lymphocytes (IELS), which are white blood cells found in the immune system. More than 25 IELS per 100 epithelial cells is significant. Epithelial cells line your intestines and act as a barrier between the inside and the outside of your body.
  • Crypt hyperplasia with a decreased villi/crypt ration. Crypts are grooves between the villi, which are the small fingerlike projections that line the small intestine and promote nutrient absorption. Crypt hyperplasia is when the grooves are elongated compared to a normal intestinal lining which has short crypts.
  • Blunted or atrophic villi. This is a shrinking and flattening of the villi due to repeated gluten exposure.
  • Mononuclear cell infiltration in the lamina propria. The lamina propria is a thin layer of loose connective tissue, which together with the epithelium forms the mucosa which stops pathogens from entering the body.
  • Epithelial changes, including structural abnormalities in epithelial cells.

The endoscopy itself may show scalloping and/or flattening of dudodenal folds, fissuring over the folds, and a mosaic pattern of mucosa of folds.

Modified Marsh Classification of Histologic Findings in Celiac Disease

The World Gastroenterology Organization recommends pathologists use a modified Marsh classification for interpretation. Dr. Michael Marsh introduced the classification system in 1992 to describe the stages of damage in the small intestine as seen under a microscope, also known as histological changes. Originally the Marsh Types ranged from 0 to 4, with a type of 3 indicating celiac disease. It has since been simplified to allow for a greater degree of consistency and reproducibility between pathologists.

Modified Marsh Classification of histologic findings in celiac disease (Oberhuber)

Marsh Type IEL / 100 enterocytes – jejunum* IEL / 100 enterocytes – duodenum* Crypt hyperplasia Villi
0 <40 <30 Normal Normal
1 >40 >30 Normal Normal
2 >40 >30 Increased Normal
3a >40 >30 Increased Mild atrophy
3b >40 >30 Increased Marked atrophy
3c >40 >30 Increased Complete atrophy
*IEL/100 enterocytes – intra-epithelial lymphocytes (IELS) per 100 enterocytes (epithelial cells in the small intestine)
  • Type 0: Intestinal lining is normal -celiac disease highly unlikely
  • Type 1: Intestinal lining has been infiltrated with IELS – seen in patients on a gluten free diet (suggesting minimal amounts of gluten or gliadin are being ingested), patients with dermatitis herpetiformis and family members of celiac disease patients. This may also indicate gastroduodenits caused by H. pylori, hypersensitvity to food, infectons (viral, parasitc, bacterial), bacterial overgrowth, pharmacological drugs (mainly NSAIDs), IgA defcit, common variable immunodefciency or Crohn’s disease.
  • Type 2: Very rare, seen occasionally in dermatitis herpetiformis.
  • Type 3: Spectrum of changes seen in symptomatic celiac disease.

Simplified systems may be more reproducible (Corazza, Roberts, Ensari)

  • Grade A/Type 1: increased intraepithelial lymphocytes but no villous atrophy
    • Seen in patients on gluten free diet (suggesting minimal amounts of gluten or gliadin are being ingested); patients with dermatitis herpetiformis; family members of celiac disease patients, not specific, may be seen in infections
  • Grade B1/Type 2: villi still present but shortened
    • Spectrum of changes seen in symptomatic celiac disease
  • Grade B2/Type 3: complete villous atrophy
    • Spectrum of changes seen in symptomatic celiac disease


Modifed Marsh classification images














What To Expect During An Endoscopy

This procedure takes a little less than thirty minutes and, for adults, sedatives and local anesthetics are used. Children are usually put under general anesthesia. During the biopsy, the gastroenterologist will insert a small tube with a camera through the patient’s mouth and into the digestive tract to the small intestine. Once there, the physician will examine the duodenum (entryway into the small intestine) and take multiple tissue samples due to the “patchy” nature of villous atrophy. The tissue samples will then be examined by a pathologist under a microscope and assigned a Marsh classification.

Since there are no nerve endings in the lining of the intestine, the procedure is not painful – though some patients may experience a sore throat.


Patients who cannot or will not tolerate an endoscopy may be given the option to undergo video capsule or “pill” endoscopy where a capsule the size of a large vitamin pill is swallowed and takes thousands of pictures of the small intestine.  However, there is no conclusive evidence that this can substitute for traditional endoscopy and biopsy.


Is Endoscopy Really Necessary if My Blood Test is Positive or I Feel Better on a Gluten-Free Diet?

The endoscopic biopsy is necessary to confirm a celiac disease diagnosis. The blood tests indicate whether there is a possibility of celiac disease but you cannot confirm the diagnosis until an endoscopic biopsy is taken, with two exceptions:

For individuals with dermatitis herpetiformis (DH), a skin biopsy is sufficient for diagnosis of both DH and celiac disease. This biopsy involves collecting a small piece of skin near the rash and testing it for the IgA antibody. It is not necessary to perform an endoscopic biopsy to establish the diagnosis of celiac disease in a patient with DH; the skin biopsy is definitive.

Learn about Dermatitis Herpetiformis (DH)

For children with symptoms and signs of malabsorption, a very high tTG-IgA titer (>10 time upper limit of normal), and a positive EMA (antiendomysial) in a second blood sample, some physicians may recommend avoiding endoscopic biopsy, and directly starting a gluten-free diet. Others may recommend genetic testing for additional confirmation. Resolution of symptoms while on a gluten-free diet may be used to confirm the diagnosis.

Learn about Celiac Disease Screening


Currently, the only treatment for celiac disease and non-celiac wheat sensitivity is lifelong adherence to a strict gluten-free diet. People living gluten-free must avoid foods with wheat, rye and barley, such as bread and beer. Ingesting small amounts of gluten, like crumbs from a cutting board or toaster, can trigger intestinal damage.

Learn about the Gluten-Free Diet

Annual Follow-Up

Once diagnosed, annual follow-up with your physician is necessary to monitor nutritional deficiencies and your compliance with a gluten-free diet, as well as assess for associated conditions.

Learn about Annual Follow-Up

Finding the Right Doctor

Celiac Disease Foundation can help you find the right doctor to discuss symptoms, diagnose, and treat celiac disease. Our nationwide Healthcare Practitioner Directory lists primary care physicians and specialists,and dietitians and mental health professionals, experienced in celiac disease and non-celiac wheat sensitivity.

Find a Healthcare Practitioner

Fernández Bañares F, Mariné M, Rosinach M, Carrasco A, Esteve M. Type 1 Marsh Celiac Disease: Diagnosis and Response. In Rodrigo L and Peña AS, editors. Celiac Disease and Non-Celiac Gluten Sensitvity. Barcelona, Spain: OmniaScience; 2014. p. 289-302.
Stanford Medicine Surgical Pathology Criteria: Celiac Disease. Accessed Aug. 30, 2016.