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Endoscopic Biopsy

To confirm a celiac disease diagnosis, your doctor may recommend an upper gastrointestinal endoscopy. This procedure will allow your doctor to identify any inflammation or damage in your small intestines, which is a sure sign of celiac disease. Your doctor will take a small biopsy of your intestines during the endoscopy, which will help to confirm your diagnosis. In order for the endoscopy to be accurate, the patient must be on a gluten-containing diet.

An endoscopy may sound like a big procedure, but it only takes about 15 minutes and is a low-risk procedure.

Why It’s Recommended

While blood tests are helpful in diagnosing celiac disease, they aren’t perfect. False negatives and false positives are possible, so an endoscopy is needed.

In the small intestine, there are finger-like projections called “villi” that help you absorb nutrients. In individuals with celiac disease, gluten damages the villi and causes them to flatten. As a result, the body can’t get the nutrients it needs, which leads to many of the health problems associated with celiac disease. With a biopsy, doctors can see if the villi are flattened.

Endoscopy has long been known as the “gold standard” for celiac disease diagnosis. As blood testing improves, endoscopy may be needed less and less, but for now it remains essential.


The actual procedure does not take long, but you will need to take some time to properly prepare. Your doctor will give you a full set of instructions to follow in preparation for the endoscopy, and certain instructions will be dependent upon your age. Here are some brief details of what you can expect.

You will be asked to fast (no food or drink) for 6-8 hours before your endoscopy. This will ensure that your stomach is empty for the procedure. You may also be asked to stop taking certain medications, such as anti-clotting drugs, for a certain period of time before the procedure.

Before the endoscopy begins, you will be sedated and the amount and type of sedation will depend on your age and any other co-existing medical conditions. Sometimes you will be given an anesthetic to numb your throat in addition to the sedative. You will be asked to lie on your back or on your side for the procedure.

During the Endoscopy

During the endoscopy, your doctor will snake a very thin tube through your mouth. When the tube reaches your small intestine, a small tool will be used to take four to eight biopsies from your intestinal wall. After the procedure, a pathologist will use a microscope to examine the extent of damage to the villi. If your villi appear flattened or damaged, it is likely that celiac disease is the cause.

After the Endoscopy

Following the procedure, you will be transferred to a recovery room until any medication or sedative wears off. You may have a mild sore throat or feel slightly bloated as a result of the procedure, but those sensations usually clear up quickly. Most individuals are able to resume eating food within a few hours, after they are fully recovered.

Endoscopy Results

Often, doctors are able to view the image results of an endoscopy that day. But in the case of celiac disease, it’s the actual biopsy results that your physician is most interested in. Therefore, you may be asked to schedule an appointment to go over the results at a later date since it may take a few days for the pathology department to return the biopsy results to your physician.

Positive Test Result

If you test positive for celiac disease, you will need to manage a strict gluten-free diet. Learn more about managing the gluten-free diet here.

Negative Test Result

If your small intestinal biopsy results indicate that celiac disease is not present, but you and your doctor still suspect gluten is the cause of your symptoms, you may want to explore the possibility of non-celiac gluten sensitivity (‘gluten sensitivity’). Learn more about gluten sensitivity here.

Potential celiac disease is also an option. This is a term used when an individual has a positive celiac disease blood test but a normal small intestinal biopsy. People with potential celiac disease are at an increased risk for developing celiac disease as indicated by positive celiac disease blood tests. This means that they may transition into developing active celiac disease, which is marked by intestinal damage.

At this time, there are no universal guidelines on treating potential celiac disease with a gluten-free diet and most physicians recommend continuing with a regular gluten-containing diet.

Because active celiac disease may develop over time, it is important for individuals with potential celiac disease to monitor any changes in their health such as new signs or symptoms that may indicate celiac disease.

Talk to your doctor about other reasons for your negative biopsy test results and what, if any, future follow-up tests are recommended for you.

What some celiac disease experts are saying about potential celiac disease:

“If the celiac disease blood test is abnormal but their biopsy is negative, I will place a child who has growth failure and is close to puberty on a gluten-free diet and will then have the child undergo a gluten challenge after his or her growth has occurred. This cuts down on the possibility of a child’s growth being stunted for life. This practice is relatively common in pediatrics where a child’s growth is so critical, and if you miss the window of opportunity prior to puberty you lose height for life.”

– Dr. Ritu Verma, Director of the Center for Celiac Disease at The Children’s Hospital of Philadelphia and member of NFCA’s Scientific/Medical Advisory Council

“The threshold for treatment in childhood should be lower than for adults with the understanding that this group of biopsy negative symptomatic children should probably carry an indeterminate diagnosis and be challenged in early adulthood.”

– Dr. Dan Leffler, Director of Clinical Research at the Celiac Center at BIDMC and member of NFCA’s Scientific/Medical Advisory Council

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