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GI Procedures: What to Expect

Children’s Mercy can provide all the gastrointestinal (GI) procedures your child may need so their health care team can understand and treat their condition. With a team of specialists who love working with kids and teens, we can help your child have a comfortable and safe experience during their procedure.  

Every child is unique, and not all procedures may be appropriate for your child’s needs. If you have questions about a specific procedure, talk to your gastroenterology team.

Supportive care during procedures 

We want to make you and your child comfortable during all procedures. All of our anesthesiologists are experts in finding the just-right dose of medication for children of all ages and sizes. Our Child Life specialists can help prepare your child for what to expect in an age-appropriate way and make sure they have their questions answered. We’ll keep you up to date along the way and in most cases, your child can go home the same day after their procedure.

Find out more about supportive care during GI procedures at Children’s Mercy.


An endoscopy is a medical procedure where a doctor uses a flexible tube with a light and camera attached (an endoscope) to look inside your child’s digestive tract. Your child is asleep under anesthesia during this procedure. Many procedures to diagnose and treat GI conditions can be completed through an endoscopy.

Each year, more than 5,000 families trust Children's Mercy when their child needs an endoscopy procedure. Our anesthesiologists will work with your child to keep them comfortable and safe during their procedure.

How does an endoscopy work?

The endoscope enters through the mouth for an upper endoscopy (EGD). This procedure allows the doctor to see the inside of the esophagus, stomach, and the upper part of the small intestine. 

The endoscope enters through the anus for a colonoscopy. This allows the doctor to see the large intestine (colon). 

In addition to providing detailed images of the inside of the digestive tract, the doctor can also pass special instruments through the tube of the endoscope to take tissue samples for biopsy and perform other procedures.

Procedures performed through endoscopy  

An esophago-gastro-duodenoscopy (EGD) is also known as upper endoscopy procedure. The GI doctor will carefully push the endoscope through the mouth, esophagus, stomach and the first part of the small intestine. They can then take pictures and tissue samples (biopsies) to help them diagnose and treat many GI conditions, such as gastroesophageal reflux disease (GERD), ulcers, foreign body removals, inflammation, celiac disease, and strictures or narrowing of the esophagus.

An EGD is typically an outpatient procedure that takes 20-30 minutes. Afterwards, your child may feel sleepy and should rest at home the remainder of the day, but generally can return to normal activities the following day.

A capsule endoscopy allows your child’s doctor to see the middle part of the GI tract (the small intestine) using a tiny camera inside a pill-sized capsule. This is especially helpful because that area can’t be seen with traditional upper endoscopy or colonoscopy procedures. The capsule can either be swallowed or placed by endoscopy, depending on your child’s age and abilities, and it passes through their system and is excreted in a bowel movement.

There are usually two steps to the process of a capsule endoscopy. The first one is called a patency capsule. This is a “practice run” to ensure that there are no narrow spots, called strictures, in your child’s intestine that would block the capsule from safely passing through the entire digestive tract.

There are some dietary restrictions around the patency capsule procedure, but it is usually fairly straightforward. Once your child has swallowed the capsule, we will take an x-ray to ensure it has reached the colon.

If the patency capsule successfully passes through your child’s digestive tract, your doctor may proceed to a small bowel capsule endoscopy. The process for this procedure is very similar to the patency capsule, except the pill-shaped device will contain a small camera and light source to take pictures of the small intestine. These images are recorded by a tracking device that your child will wear on a belt during the monitoring period. Afterwards, your child’s doctor will review the images and share the results with you at a follow-up appointment.

During a colonoscopy, the GI doctor will carefully pass the endoscope into your child’s rectum (bottom) and along the entire large and small intestine. They can then take pictures and tissue samples (biopsies) to investigate the causes of abdominal pain, diarrhea, or blood in the stool.

Colonoscopy can help your doctor diagnose conditions like inflammatory bowel disease or polyposis, and they can remove polyps during the procedure if needed.

A colonoscopy is typically an outpatient procedure that takes 30-60 minutes. Your child will need to follow special preparation instructions for a few days before the procedure to clean out the bowel as much as possible. Most children will need to rest for the remainder of the day after the procedure, but generally feel better by the following day.

A double balloon enteroscopy (DBE) is a procedure that uses a special scope (a long flexible tube with a camera at the end) and a long plastic overtube to examine and endoscopically treat any abnormalities found in the small intestine (small bowel). This special instrument uses two balloons that alternately inflate and deflate like an accordion to move forward deep within the small intestine.

The DBE scope enters either through the mouth or rectum to examine the small bowel. Due to the extensive nature of the procedure, it takes about three to four hours to complete. 

DBE is used to diagnose and treat several conditions, including polyps (primarily Peutz-Jeghers Syndrome), bleeding and inflammatory bowel disease.  Often, a DBE helps the doctor further investigate things noted on previous studies, such as a capsule endoscopy or MRI of the abdomen.

If your child is having an upper double balloon endoscopy only, they need to stop eating by midnight prior to the procedure. If your child is having a lower double balloon endoscopy, they will need to do a bowel clean-out similar to a colonoscopy clean-out. They will not be able to eat any solid food the day before the procedure and will need to do a prep that completely cleans out the small bowel and colon. 

Most children are back to normal in the next day or two. Depending on what treatment is done during the DBE, some children need more time to recover at home.  

A BRAVO pH test is a way to discover the amount of acidity in a child’s esophagus to determine whether they have gastroesophageal reflux disease (GERD). The BRAVO capsule is a small device, like a pill, that is attached to the esophagus during an EGD (upper endoscopy). 

The day of the study, your child will come to Children’s Mercy’s outpatient surgery area so an experienced GI doctor can place the capsule via endoscopy. The BRAVO study uses a wearable monitoring device which will record all data for the 48-hour duration.  

A BRAVO capsule test is available for children four years of age and older. Your child will need to stop taking any antacid medications 72 hours prior to the procedure.

Most children are able to go home the same day after the capsule is placed. There may be some throat discomfort with this study, as there is a small device in your child’s throat. However, the device is very small and will not cause any problems related to eating or physical activity. There are a few dietary restrictions with this test, but generally your child can return to normal diet and activity following the procedure.

The day of the procedure, your care team will teach you how to use the monitoring device. The recording monitor must always stay within three feet of your child. There are several buttons on the monitor that will need to be pushed throughout the duration of the study. The child can attend school during the study.

The capsule will pass through the digestive system on its own within seven days or so after it was placed. You will return the monitoring device at your clinic appointment 48 hours after placement, and results from the BRAVO pH test will be available within two weeks of the procedure date. 

Polypectomy refers to the removal of polyps during endoscopy. This can take place during upper endoscopy (where the endoscope enters through the mouth, also called an EGD), colonoscopy (where the endoscope enters through the anus) or during double-balloon enteroscopy.  

A polyp is a small growth of tissue in the lining of the GI tract. Many polyps are benign (not harmful), but often the doctor will remove them if there is any concern that they might become cancerous. 

Your child’s doctor can remove a polyp by encircling it with a wire and using a gentle electrical current to remove the tissue that is jutting out. The tissue that is removed is recovered through the endoscope, whenever possible, so that it can be examined under the microscope to make sure that there are no features of cancer. 

Polypectomy can be done during any endoscopic procedure if your doctor encounters an intestinal polyp. Sometimes, if the polyp is especially large or in a difficult location, it may require a second procedure to safely remove it. Removing a polyp is important to make sure that there is no evidence of cancer and to limit bleeding and in some cases, abdominal pain. 

In most cases, children do not need to be admitted unless there is more than slight to moderate bleeding. However, because tissue is being cut, there is an increased risk of bleeding with each polypectomy. If a child has numerous polyps that need to be removed, they may have a more significant risk (greater than 1%) of bleeding immediately after the procedure.

In most cases, bleeding can just be observed, but occasionally, your doctor will need to perform a second procedure. Very rarely, a blood transfusion or surgery is required.

Children undergoing endoscopy with polypectomy generally recover the same as those who had an endoscopy without polypectomy. While polypectomy slightly increases the time needed for the procedure, it does not cause any additional pain or discomfort for your child. 

Dilation is the process during which an area of the intestine which is too narrow can be stretched out. 

It can help with several types of conditions that can result in narrowing of the intestinal tract, including inflammatory bowel disease, eosinophilic esophagitis and others.

Most of the time, your child’s doctor will use a small balloon, or several balloons, that can be passed through the endoscope to the area that needs to be stretched out. Then, as the balloons are inflated (one after the other), the area of bowel in front of the scope is slowly opened up, or dilated. Dilation can be performed during any endoscopic procedure. 

Most children can go home the same day after a dilation procedure. In some cases, the doctor may want them to stay overnight for observation, but in general, the recovery from dilation is the same as for routine endoscopy. 

Children swallow a variety of objects. In many cases, under the guidance of your physician, you can safely “wait and watch” as the object passes through the intestine and out in a bowel movement. However, sharp objects, batteries, toy magnets and any objects which stay in the stomach for a long period of time may need to be removed by endoscopy. It’s important to remove the foreign body in a timely manner to decrease the risk of obstruction or damage to the intestine.

Foreign bodies can be removed during both upper and lower endoscopies (EGD or colonoscopy). The procedure lasts less than 30 minutes and in most cases, your child can go home the same day. Recovery is the same as for routine endoscopy and colonoscopy. The risks of the procedure are similar to routine endoscopy but there is an increased risk of bleeding or trauma while removing the foreign body, depending on its shape, size and location in the digestive tract.

Some children develop bleeding in their intestines. Most of the time, the bleeding is slow and your child’s doctor will do an endoscopy to determine the cause. In rare cases where there is significant bleeding that does not respond to medications, your doctor may perform an endoscopy to try to stop it.

During endoscopy there are several options to stop bleeding, including:

Cautery (ERBE®) — passing electricity around the tissue that is bleeding to stop the bleed by burning the superficial layers of the intestine

Endoclips — using small metal clips passed through the endoscope to close off a bleeding blood vessel

Hemospray® — a special spray that coagulates blood (forms a clot) so that bleeding is stopped. Children’s Mercy is one of the few pediatric hospitals in the country to be able to use Hemospray. In some cases, this is the only option available to stop bleeding in the intestines, short of major surgery.

A hepatologist (liver specialist) can perform a ligation, or closing off, of blood vessels that are causing bleeding in a child’s esophagus. They usually do this by looping surgical thread around the vessel and tying it tightly to prevent further bleeding. The procedure is common in children with portal hypertension who have varices (abnormal blood vessels) that have formed in the esophagus.

The procedure normally takes less than an hour, but depending on the child’s condition, they may need to stay overnight in the hospital afterwards.

While most endoscopy procedures require your child to be asleep under anesthesia, an unsedated transnasal endoscopy (TNE) allows the doctor to safely examine your child’s esophagus while they are awake. 

The doctor will give your child a local numbing medicine for their nose and throat. Then, they will use a very small scope that enters through the nose to look at the inside of the esophagus. 

Since TNE only requires topical anesthetic, it can be performed in an office setting rather than requiring a procedural or surgical suite. This procedure is shorter and much easier for children with eosinophilic esophagitis (EoE) and other conditions that require frequent endoscopies. Currently, Children’s Mercy is one of only a few children’s hospitals that offer this procedure. It is available for children ages 8 and older.

Benefits of TNE include decreased possibility of side effects and complications due ot anesthesia, enhanced patient and family experience, and reduced risk of infection through single-use scopes.


Additional procedures to diagnose GI conditions

A pH probe study helps your doctor understand the frequency, duration and severity of acid reflux—when contents from the stomach enter your child’s esophagus (food pipe).

During a pH probe study, your child will stay in the hospital for about 24 hours. A technician will place a thin, flexible probe with sensors attached into your child’s nose and down their throat. An x-ray helps us be sure the probe is in the right place for the most accurate test results. The probe is connected to a monitoring device to keep track of the acidity levels in the esophagus over the testing period. Your family will also help by recording when your child experiences reflux symptoms during the test.

A rectal suction biopsy uses a device to obtain a small piece of tissue from your child’s rectum. It is primarily a test for Hirschsprung’s disease.

This procedure does not hurt and can usually be done while your child is awake, unless they are having other endoscopy procedures at the same time. Your child will need to avoid eating or drinking for two hours before the procedure. The test itself takes about 10-15 minutes, and we will observe your child for about 30 minutes afterwards to check for excessive bleeding, which is rare.

A hydrogen breath test can help your child’s doctor determine whether your child is sensitive to sugar substances such as lactose, glucose, or fructose. Often, the doctor will order this test when your child is having symptoms such as stomach pain or upset after eating foods containing those sugars. By testing the levels of hydrogen in your child’s breath before and after eating the suspected substance, we can better understand how their body processes the sugars.

A nurse will call to give you specific instructions about how to prepare for the test, which includes specific dietary restrictions for the day before the test. When you arrive at the testing area, your child will breathe into a bag and the air from the bag will be put into a machine that analyzes the breath. After breathing into the bag twice, your child will drink a prepared drink that contains the type sugar we are testing. Then, they will breathe into the bag at specific intervals so we can measure for the presence of hydrogen, which indicates a problem with digesting the sugar.

Expect to spend about 4-5 hours in clinic for the testing. Once the testing is complete, your doctor will analyze the results and talk with you about a plan of care.