How Do Doctors Check The Small Intestine? Key Facts

Doctors examine the small intestine using a long, flexible tube with a camera, called an endoscope. The most common method is an upper endoscopy, where the scope is passed through the mouth and stomach into the first part of the small intestine. For deeper sections, doctors use a specialized balloon endoscope or a capsule camera that you swallow. These procedures allow doctors to see inflammation, ulcers, bleeding, and other problems directly.

What Is an Upper Endoscopy (EGD)?

An upper endoscopy is the standard first step for looking at the small intestine. The medical name is esophagogastroduodenoscopy, often shortened to EGD. The name describes the path: esophagus, stomach, and duodenum, which is the first section of the small intestine.

During the procedure, you lie on your side. You receive sedation through an IV so you stay relaxed and comfortable. The doctor guides a thin, flexible tube with a high-definition camera through your mouth, down your esophagus, and into your stomach and duodenum. The tube does not interfere with breathing. The procedure typically takes 15 to 30 minutes.

An EGD can only reach the duodenum, which is about the first 20 to 25 centimeters of the small intestine. The small intestine is roughly 6 meters long in total. So an EGD gives doctors a clear view of the beginning, but not the rest.

During an EGD, the doctor can take tissue samples called biopsies. This is painless because the intestine has no pain receptors. Biopsies help diagnose conditions like celiac disease, Crohn’s disease, and certain infections.

How Do Doctors Check the Small Intestine Beyond the Duodenum?

The middle and lower portions of the small intestine — the jejunum and ileum — are harder to reach. Standard endoscopes are too short. For these areas, doctors use specialized techniques.

Balloon enteroscopy is one option. The doctor uses a longer scope with a balloon attached to the tip. The balloon inflates to grip the intestinal wall, allowing the scope to be pushed further in. There are two types: single-balloon and double-balloon enteroscopy. These procedures take longer, often 60 to 90 minutes, and usually require deeper sedation. They allow the doctor to see the entire small intestine, take biopsies, and treat bleeding or polyps.

Capsule endoscopy is another method. You swallow a small pill-shaped camera, about the size of a large vitamin. The camera takes thousands of pictures as it travels naturally through your digestive tract over 8 to 12 hours. You wear a sensor belt that records the images. The capsule passes out of your body in a bowel movement, usually within 24 to 48 hours.

Capsule endoscopy is excellent for finding hidden bleeding, Crohn’s disease, and tumors. But the doctor cannot take biopsies or treat anything during this test. If the capsule finds a problem, a balloon enteroscopy may follow for treatment or tissue sampling.

What About Imaging Tests Like CT and MRI?

Imaging tests do not show the inside of the intestine directly. Instead, they create detailed pictures of the intestine and surrounding organs from outside the body. These tests help doctors see thickening of the intestinal wall, narrowing, fistulas, and masses.

CT enterography is a computed tomography scan with a special contrast material. You drink a large volume of liquid contrast before the scan. This liquid stretches the small intestine so the walls are easier to see. The CT scanner then takes cross-sectional images. It is quick, usually done in under a minute of scanning time.

MR enterography uses magnetic resonance imaging instead of radiation. It also requires drinking contrast liquid. MR enterography takes longer, often 30 to 45 minutes, and requires lying still inside a narrow machine. It is often preferred for younger patients because it avoids radiation exposure, and it is especially useful for monitoring Crohn’s disease.

Imaging tests cannot detect subtle surface problems like mild inflammation or flat lesions. The intestinal lining is not directly visible. For that reason, imaging and endoscopy are complementary. Doctors often use imaging first for a broad view, then endoscopy for a detailed look.

Which Test Is Right for Which Symptoms?

The choice of test depends on your symptoms and what your doctor suspects.

• Heartburn, difficulty swallowing, or upper abdominal pain: Upper endoscopy is the standard choice.
• Suspected celiac disease: Upper endoscopy with biopsies of the duodenum is the diagnostic standard.
• Unexplained bleeding or anemia: Upper endoscopy and colonoscopy come first. If both are normal, capsule endoscopy is the next step to look at the small intestine.
• Suspected Crohn’s disease involving the small intestine: MR enterography or capsule endoscopy are common options. Balloon enteroscopy with biopsies may confirm the diagnosis.
• Known polyps or tumors in the small intestine: Balloon enteroscopy allows direct viewing and removal or biopsy.

Your doctor will also consider your overall health. Sedation carries some risk, especially for older adults or those with heart or lung conditions. Imaging tests avoid sedation but may require contrast dye, which can affect kidney function.

How Should You Prepare for These Procedures?

Preparation depends on the specific test. Your doctor will give you detailed instructions. Following them matters because a poorly prepared intestine can hide problems.

For an upper endoscopy, you must fast for about 8 hours before the procedure. This means no food or drink. An empty stomach gives the doctor a clear view and reduces the risk of vomiting during sedation.

For balloon enteroscopy, preparation is more involved. The entire small intestine needs to be clear of food. You may need a liquid diet for one to two days before, followed by a laxative preparation similar to what is used before a colonoscopy.

For capsule endoscopy, you typically fast overnight. After swallowing the capsule, you wait about two hours before drinking clear liquids and about four hours before eating a light meal. You may need to avoid certain medications, especially iron supplements, for a few days beforehand.

For CT or MR enterography, you usually fast for 4 to 6 hours before the scan. You will drink the contrast liquid over about 45 to 60 minutes before imaging begins.

What Are the Risks and Recovery Times?

All medical procedures carry some risk. Understanding the actual risks helps you make an informed decision.

Upper endoscopy is very safe. The main risks are reactions to sedation, bleeding at a biopsy site, and a rare perforation, which is a tear in the intestinal wall. Perforation occurs in fewer than 1 in 1,000 procedures. Most people recover quickly and can return to normal activities the next day. You cannot drive for 24 hours after sedation.

Balloon enteroscopy carries a slightly higher risk of perforation because the scope travels deeper and the balloon stretches the intestine. The risk is still low, estimated at around 1 in 200 to 1 in 300 procedures. Recovery is similar to upper endoscopy, though the procedure takes longer.

Capsule endoscopy has one main risk: the capsule becoming stuck. This happens in about 1 to 2 percent of procedures. The capsule may lodge in a narrowed area of the intestine, often due to undiagnosed Crohn’s disease or a stricture. If the capsule does not pass within a few days, imaging can locate it. In some cases, a balloon enteroscopy or surgery is needed to remove it. Signs of blockage include severe abdominal pain, vomiting, or bloating.

CT scans expose you to ionizing radiation. The dose from one CT enterography is roughly equivalent to a few years of natural background radiation. MR enterography avoids radiation but carries risks from sedation if needed, and the contrast agent gadolinium is generally avoided in pregnancy.

What Happens After the Tests?

Your doctor will explain the findings and what they mean. If biopsies were taken, results typically take several days to a week. The pathologist examines the tissue under a microscope to look for specific changes.

Normal results mean no visible problems. But absence of visible disease does not always mean the intestine is fully healthy. Some conditions, like microscopic colitis, only appear under a microscope. Others, like functional disorders, show no structural abnormality at all.

Abnormal results guide the next steps. If a bleeding site is found, it may be treated during the same procedure. If inflammation is present, the pattern helps distinguish between Crohn’s disease, celiac disease, infections, and medication-related injury. If a mass or polyp is found, biopsy results determine whether it is benign or malignant.

Follow-up depends on the diagnosis. Some conditions require repeat endoscopy to monitor treatment response. Celiac disease, for example, may warrant a follow-up endoscopy after months on a gluten-free diet to confirm healing. Your doctor will set a schedule based on your specific situation.