Diagnosing Crohn’s Disease in Children

Gastroenterologists at Hassenfeld Children’s Hospital at NYU Langone diagnose Crohn’s disease in children. A type of inflammatory bowel disease, or IBD, this condition typically affects the end of the small intestine, called the ileum, and the beginning of the large intestine, or colon. However, it can cause inflammation anywhere in the gastrointestinal tract, from the mouth to the anus. It can also affect more than one segment of the gastrointestinal tract, creating diseased areas between healthy ones.

Crohn’s disease often involves flare-ups in periods of remission, which is an absence of symptoms.

Common symptoms and complications of Crohn’s disease can include diarrhea, abdominal pain, weight loss, and dehydration. The condition may also lead to fistulas, which are tunnels that form in the intestinal wall or anus that lead to surrounding tissues or organs. Anal skin tags, which are flaps of skin on the anus, can also occur. Crohn’s disease can interfere with proper growth and lead to delayed puberty in some children.

Another form of IBD, ulcerative colitis, can cause similar symptoms. However, that condition typically affects only the large intestine. IBD is not the same as irritable bowel syndrome, or IBS, which is a collection of symptoms—such as abdominal cramps, constipation, and diarrhea—that occur together. Unlike inflammatory bowel disease, IBS does not cause inflammation that damages the gastrointestinal tract.

The causes of Crohn’s disease are not known, though it’s thought to result from a combination of influences, including an autoimmune reaction, genetics, and the environment.

Our doctors perform a physical exam and testing to diagnose Crohn’s disease in children.

Medical History

Your child’s doctor asks about symptoms and their frequency and severity. You may be asked about the types of food your child eats and if his or her diet has changed recently.

Physical Exam

To help reach a diagnosis, your child’s specialist asks whether your child has experienced loss of appetite, abdominal pain, and diarrhea. The doctor checks your child’s temperature and measures his or her height and weight. This is because Crohn’s disease can cause slowed growth and weight loss.

Diagnostic Tests

Your child’s doctor may conduct several tests to make a diagnosis.

Blood Tests

Blood tests help your child’s doctor look for signs of inflammation and anemia, which is a reduction in the number of red blood cells.

Crohn’s disease can affect the liver’s ability to make proteins and filter toxins from the body. For this reason, your child’s doctor may recommend liver function tests.

Because this condition can prevent the absorption of vitamins and other nutrients from the intestine into the bloodstream, levels of iron, folate, vitamin B12, and vitamin D may be tested.

Stool Tests

Crohn’s disease affects the frequency and consistency of bowel movements. A stool test may be performed to check for the presence of blood and infection-causing bacteria, such as Clostridium difficile, commonly known as C. difficile or C. diff. This bacterium can attack the lining of the intestines.

The doctor gives you a small plastic container that you use to collect a sample of your child’s stool. You then return this sample or send it directly to a laboratory for analysis.

Digital Rectal Exam

A doctor may perform a digital rectal exam to look for signs of Crohn’s disease. In this brief exam, the doctor inserts a gloved finger into the rectum to check for blood and tenderness.

Upper Endoscopy

Your child’s doctor may recommend an upper endoscopy, which allows the doctor to check the lining of the esophagus, stomach, and small intestine for inflammation, bleeding, ulcers, or obstructions. It is performed with general anesthesia.

During this test, the doctor inserts an endoscope, a thin, flexible instrument with a camera at its tip, into the throat and advances it through the esophagus to the stomach and small intestine. Your child’s doctor then views the live images on a monitor.

An upper endoscopy typically takes 10 to 20 minutes.


Gastroenterologists typically recommend a colonoscopy to diagnose Crohn’s disease. In this test, live images of the colon and rectum enable the doctor to examine the intestinal lining for inflammation.

Before the procedure, a doctor asks that your child avoid eating solid food for 24 hours. He or she may have clear liquids, such as apple juice or ginger ale, until four hours prior to the procedure. Babies younger than 12 months may have breast milk or baby formula. Your child’s doctor supplies a laxative solution to drink the night before, so the bowels are empty during the exam.

To perform a colonoscopy, your child’s doctor inserts a colonoscope, a long, thin, flexible instrument with a camera and light embedded in the tip into the anus and slowly moves it through the rectum and colon. Images of the colon are displayed on a nearby computer monitor.

The procedure typically takes about 30 minutes and requires general anesthesia.

During this test, a doctor may perform biopsies, removing small tissue samples from the colon and sending them to a laboratory for analysis. These results may help doctors differentiate between Crohn’s disease and ulcerative colitis.

Capsule Endoscopy

A gastroenterologist may perform a capsule endoscopy to examine the small intestine. Much of this organ is inaccessible using other types of tests. A capsule endoscopy can help doctors determine if Crohn’s disease is the cause of symptoms.

In this procedure, a doctor asks the child to swallow a capsule about the size of a multivitamin that has a tiny camera inside. The camera takes thousands of pictures as it passes through the small intestine. These images are transmitted via radio waves to a small receiver worn on a belt around the waist. A doctor downloads the images for review.

If a child cannot swallow the capsule, it is placed in the duodenum at the top of the small intestine during an upper endoscopy.

The capsule passes through the gastrointestinal tract and leaves the body during a bowel movement and can be flushed down the toilet.

Magnetic Resonance Enterography

Your child’s doctor may use magnetic resonance enterography, a type of MRI scan performed with a contrast material, that produces detailed images of the small intestine. An MRI uses a magnetic field and radio waves to create two- and three-dimensional images of the small and large intestines.

Your child drinks a flavored contrast agent or a dye prior to this MRI scan to highlight the intestine during the test, which takes 45 to 60 minutes. To help small children remain still during the test, a pediatric anesthesiologist may recommend sedation.

Bone Density Testing

Children with Crohn’s disease are prone to experiencing a loss of bone mass. This may be caused by elevated levels of proteins called cytokines, which increase inflammation in the body. Treatment with corticosteroids can also affect the formation of bone. If your child has taken these medications or if he or she has experienced weight loss or other signs of malnutrition, a doctor may recommend a bone density test called a dual X-ray absorptiometry, or DEXA, scan.

During this test, your child lies on a table. Next, a device takes readings of bone mineral density of the spine and hip.

A doctor compares the test results with average bone densities of healthy children of the same age, gender, and ethnicity. The test takes about 20 minutes.

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