Learn about your diagnosis

Celiac disease - Small bowel -

This article will help you read and understand your pathology report for celiac disease.

by Shaheed Hakim, MD FRCPC, reviewed on November 29, 2019

Quick facts:

  • Celiac disease is a condition that develops in people who have a sensitivity to gluten.
  • Gluten causes the  immune system to damage the cells on the inside of the small intestine.
  • The damaged small intestine cannot absorb nutrients which can lead to weight loss and diarrhea.
  • When examined under a microscope, the tissue from the small bowel will show a loss of villi and increased lymphocytes.

The function and anatomy of the small intestine

The small intestine (small bowel) is a part of your gastrointestinal tract. Other parts of the gastrointestinal tract are the esophagus, stomach, colon (large bowel), rectum. Food travels into the small intestine from the stomach. The small intestine is responsible for absorbing nutrients from the food that we eat after the food is broken down in the stomach.

The small intestine is a long, thin tube that starts at the end of the stomach and ends at the colon (large bowel). Food enters the small intestine after being processed by the stomach.

The small intestine is divided into three parts:

  • Duodenum – This is the first part of the small intestine. It is connected to the stomach.
  • Jejunum – This the second or middle part of the small intestine.
  • Ileum – This is the third and final part of the small intestine. It is connected to the colon. A valve at the end of the ileum called the “ileocecal valve” stops waste in the colon from coming back into the ileum.

The inner surface of the small intestine is lined by epithelial cells that connect together to form glands. The inside surface of the small intestine is unique because it creates millions of small finger like projections of tissue called villi. Without these villi, the small intestine cannot absorb all the food we eat. Villi can only be seen when the tissue is examined under a microscope by a pathologist.


Gluten is a small molecule that is naturally found in wheat, rye, and barely. As a result, many foods such as baked goods, pastas, noodles, cereals, sauces, and alcoholic beverages contain gluten. Gluten is normally broken down in the gastrointestinal tract into smaller parts which are then absorbed by the body.

What is Celiac disease?

Celiac disease is a medical condition that develops when the body reacts abnormally to the gluten found in food. The abnormal reaction damages the cells on the inside of the small intestine. Another name for Celiac disease is gluten sensitive enteropathy.

This irritation causes small immune cells called lymphocytes to enter the space between the epithelial cells in the epithelium. Pathologists refer to this as increased intraepithelial lymphocytes.

Overtime, these immune cells damage the epithelium which causes a loss of the normal villi. Pathologists describe this change as atrophy or blunting of the villi.

A biopsy is usually performed because the patient has symptoms suggestive of Celiac disease (gluten sensitive enteropathy), which may include weakness and diarrhea. These symptoms occur when the patient eats food that contain gluten.  Biopsies are usually taken from the 2nd part of the duodenum, where the changes associated with Celiac disease are easiest to recognize.

A diagnosis of Celiac disease (gluten sensitive enteropathy) requires both clinical (serology) and pathological (biopsy) confirmation.

Your pathologist can confirm the diagnosis when they see increased intraepithelial lymphocytes in the epithelium of the small intestine, as well as the abnormal blunting or atrophy of the villi.  This blunting can further be graded as mild, moderate or severe. In severe blunting there are no villi seen and the epithelium looks flat.

Increased intraepithelial lymphocytes with no/mild villous blunting

When a tissue sample is taken from the duodenum in the early stages of the disease, the small intestine may show only mild changes including an increased number of lymphocytes in the epithelium on the inner surface of the tissue. In many early cases, the villi are still normal and the report will refer to this as ‘no or mild villous blunting’.

The finding of increased intraepithelial lymphocytes without villous blunting is not unique to Celiac disease and may be seen in other conditions. For example, Helicobacter gastroenteritis, medications (ie. Olmesartan), tropical sprue, protein intolerance, bacterial overgrowth and viral gastroenteritis all cause changes that look similar under the microscope.  Some pathologists may mention some of these conditions in the comment section.


Dysplasia refers to an abnormal pattern of growth that is initially non-cancerous but can turn into cancer. Chronic inflammation can lead to dysplasia.

The earliest change is referred to as low-grade dysplasia.  The cells in low grade dysplasia are abnormal but are still non-cancerous. In some cases, the cells become even more abnormal and progress to high-grade dysplasia. These cells look very similar to cancer cells, however, they are still only seen in the epithelium on the inner surface of the stomach.

High grade dysplasia is considered a pre-cancerous condition because it is associated with an increased risk of developing cancer in the small intestine over time. Your pathologist will closely examine the tissue for any evidence of dysplasia and will describe it in your report if it is seen.

Enteropathy-associated T-cell lymphoma (EATL)

In some patients, a gluten free diet is not enough to prevent inflammation and damage in the small intestine.  These patients are classified as having refractory celiac disease. In a specific type of refractory celiac disease, the inflammatory cells (intraepithelial lymphocytes) divide and multiply in an abnormal pattern.  This leads to a cancer called enteropathy-associated T-cell lymphoma (EATL), a type of lymphoma.

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