Small Intestine Exam: Types, What to Expect, and Why It Matters

If you're experiencing persistent digestive issues, your doctor may recommend a small intestine exam. This article explains the common types of exams, why they are performed, how to prepare, and what to expect during recovery. It also addresses common questions like why the small intestine is not checked during a colonoscopy and how to know if something is wrong.

What Is a Small Intestine Exam?

A small intestine exam is a set of diagnostic procedures used to evaluate the structure, lining, and function of the small intestine. These exams help identify conditions such as inflammation, ulcers, celiac disease, Crohn's disease, tumors, bleeding, and malabsorption issues.

View example recommendations from the InnerBuddies platform Preview the nutrition, supplement, food diary and food recipe platform recommendations that InnerBuddies can generate based on your gut microbiome test

View example recommendations →

Because the small intestine is long and coiled (about 22 feet), it can be challenging to examine fully. That's why several different methods exist, each with its own strengths and limitations.

Why Would You Need a Small Intestine Exam?

Your doctor may recommend a small intestine exam if you have red-flag symptoms such as persistent abdominal pain, unexplained weight loss, gastrointestinal bleeding, chronic diarrhea, or signs of malnutrition. More subtle clues like nausea, fatigue, food intolerances, or bloating can also prompt an evaluation.

2-minute self-check Is a gut microbiome test useful for you? Answer a few quick questions and find out if a microbiome test is actually useful for you. ✔ Takes 2 minutes ✔ Based on your symptoms & lifestyle ✔ Clear yes/no recommendation Check if a test is right for me →

How Do You Know if There Is Something Wrong With Your Small Intestine?

Symptoms of small intestine problems often overlap with other digestive disorders, making it difficult to self-diagnose. Common warning signs include abdominal pain or cramping, bloating, gas, diarrhea, constipation, fatigue, unintentional weight loss, and blood or mucus in the stool. If you experience any of these persistently, it's important to consult a healthcare professional.

Common Types of Small Intestine Exams

Here's a breakdown of the most common small intestine examinations, including what they do and what to expect.

Become a member of the InnerBuddies community Perform a gut microbiome test every couple of months and view your progress while following-up on our recommendations

Take an InnerBuddies membership →

Upper Endoscopy (EGD)

An upper endoscopy uses a thin, flexible tube with a camera (endoscope) passed through the mouth into the esophagus, stomach, and the first part of the small intestine (duodenum). It allows direct visualization of the lining and lets doctors take biopsies if needed. This procedure is performed under sedation and typically takes 15–30 minutes.

Capsule Endoscopy

Capsule endoscopy involves swallowing a small, pill-sized camera that takes thousands of pictures as it travels through your digestive tract. It is painless and allows the entire small intestine to be seen, including areas that other endoscopies cannot reach. The capsule is passed naturally in a bowel movement usually within 24–48 hours.

Discover the Microbiome Test ISO-certified EU lab • Sample stays stable during shipping • GDPR-secure data

Microbiome Test Kit →

Enteroscopy (Deep Enteroscopy)

Enteroscopy is a more advanced endoscopic technique that can reach deeper into the small intestine than a standard upper endoscopy. It can be performed via the mouth, nose, or rectum, and allows for both diagnosis and treatment (such as removing polyps or stopping bleeding). This procedure requires sedation and a longer recovery time.

Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) Scan

MRI and CT scans are non-invasive imaging techniques that create detailed cross-sectional images of the small intestine and surrounding organs. They are especially useful for detecting structural abnormalities, inflammation, fistulas, or masses. You may be given a contrast solution to drink beforehand to enhance the images.

View example recommendations from the InnerBuddies platform Preview the nutrition, supplement, food diary and food recipe platform recommendations that InnerBuddies can generate based on your gut microbiome test

View example recommendations →

Barium X-Ray (Small Bowel Follow-Through)

In a barium X-ray, you drink a chalky liquid containing barium, which coats the lining of the small intestine and makes it visible on X-ray images. A series of X-rays are taken over several hours as the barium moves through. This test can reveal blockages, narrowing, or abnormal contractions.

Functional Tests (Motility and Absorption)

These tests evaluate how well the small intestine moves food along (motility) and absorbs nutrients. They include hydrogen breath tests for sugar malabsorption or bacterial overgrowth, and stool tests that measure fat content. These are less invasive and can provide valuable functional information.

Become a member of the InnerBuddies community Perform a gut microbiome test every couple of months and view your progress while following-up on our recommendations

Take an InnerBuddies membership →

Why Isn't the Small Intestine Checked in a Colonoscopy?

A colonoscopy only examines the large intestine (colon) and the very end of the small intestine (terminal ileum). The small intestine is too long and complex to be fully visualized with a standard colonoscope. That's why dedicated small intestine exams like capsule endoscopy or enteroscopy are needed to assess this part of the digestive tract.

Preparation: What to Do Before a Small Intestine Exam

Proper preparation is critical for a successful exam. Always follow your doctor's specific instructions. General steps may include:

Discover the Microbiome Test ISO-certified EU lab • Sample stays stable during shipping • GDPR-secure data

Microbiome Test Kit →

• Fasting: You may need to avoid food and drink for 8–12 hours before the procedure.
• Medication adjustments: Some medications, especially blood thinners or diabetes drugs, may need to be paused or adjusted.
• Bowel prep: For capsule endoscopy or enteroscopy, you may be given a laxative solution to clear the intestine.
• Dietary restrictions: You may be asked to follow a low-fiber or clear-liquid diet for a day or two before.
• Arrange transportation: If sedation is involved, you will need someone to drive you home.

What to Expect During the Exam

The experience varies depending on the exam type:

• Endoscopy/Enteroscopy: You'll receive sedation through an IV, making you drowsy. The scope is gently inserted through the mouth or rectum. You may feel some pressure or cramping, but not pain.
• Capsule endoscopy: You swallow the capsule with water. You'll wear a sensor belt that records images. You can go about your day and return later to have the data analyzed.
• Imaging tests: You lie on a table inside the scanner. You may be asked to hold your breath at times. The procedure takes about 30–60 minutes.
• Barium X-ray: You drink the barium solution, which may have a chalky taste. X-rays are taken at intervals as the barium travels.

After the Exam: Recovery and Follow-Up

Recovery depends on the procedure. After sedation, you'll rest until the effects wear off, and someone should drive you home. You may experience mild bloating, cramping, or a sore throat, which usually improve within a day or two. If you notice severe pain, fever, bleeding, or difficulty swallowing, contact your healthcare provider immediately.

View example recommendations from the InnerBuddies platform Preview the nutrition, supplement, food diary and food recipe platform recommendations that InnerBuddies can generate based on your gut microbiome test

View example recommendations →

Your doctor will discuss the findings and any necessary next steps. In many cases, your exam results are combined with other information—like symptoms, lab work, and sometimes a stool test to assess your gut microbiome—to form a complete picture of your gut health.

Small Intestine Exam vs. Colonoscopy: Key Differences

Many people wonder why they need a small intestine exam when they've already had a colonoscopy. The main differences are:

Become a member of the InnerBuddies community Perform a gut microbiome test every couple of months and view your progress while following-up on our recommendations

Take an InnerBuddies membership →

• Colonoscopy examines only the large intestine and terminal ileum.
• Small intestine exams (like capsule endoscopy or enteroscopy) can visualize the entire small intestine.
• Colonoscopy is used for colon cancer screening and polyp removal, while small intestine exams target conditions like Crohn's disease, bleeding, or malabsorption.
• Both may require bowel prep, but the prep and scope path are different.

How Do I Get My Small Intestine Checked?

If you have persistent digestive symptoms, start by consulting a gastroenterologist. They will review your history, exam findings, and may order preliminary lab tests. Based on your symptoms, they will recommend the most appropriate small intestine exam—whether that's an endoscopy, capsule endoscopy, imaging, or a combination. Always follow their guidance and communicate any concerns you have about the procedure.

How a Stool Test Complements Small Intestine Exams

Small intestine exams look at structure and function, but they don't directly assess the gut microbiome. A stool test can reveal the composition and diversity of your gut bacteria, which may be relevant if you experience bloating, gas, or irregular bowel habits. Conditions like SIBO (small intestinal bacterial overgrowth) are often detected through a breath test, but a stool test can provide a broader picture of dysbiosis, or microbial imbalance.

Discover the Microbiome Test ISO-certified EU lab • Sample stays stable during shipping • GDPR-secure data

Microbiome Test Kit →

While a small intestine exam is essential for diagnosing structural and inflammatory conditions, a stool test adds a functional layer by highlighting potential microbial contributions to your symptoms. Together, they can guide more targeted lifestyle and dietary adjustments.

Key Takeaway: A Structured Diagnostic Path Leads to Better Gut Health

Understanding what a small intestine exam involves can help reduce anxiety and allow you to prepare physically and mentally. Whether your doctor recommends an endoscopy, capsule endoscopy, MRI, or another test, knowing the purpose, preparation, and what to expect afterward helps you approach it with confidence.

View example recommendations from the InnerBuddies platform Preview the nutrition, supplement, food diary and food recipe platform recommendations that InnerBuddies can generate based on your gut microbiome test

View example recommendations →

Remember that a small intestine exam is often one piece of a larger puzzle. Combining it with clinical evaluation, symptom tracking, and possibly a stool test for your gut microbiome provides a more complete view of your digestive health. This comprehensive approach supports more informed decisions and a personalized path toward better gut health.