In small bowel biopsy, a tissue sample is extracted from the small intestine, or small bowel, and sent to a laboratory for analysis. To obtain the sample, you must swallow a capsule attached to a long, thin polyethylene tube; when it reaches the small intestine, suction is applied to pull the tissue specimen into the capsule. This method permits biopsies from areas that are out of reach via esophagogastroduodenoscopy and allows for larger samples to be obtained.

Purpose of the Small Bowel Biopsy

  • To assist in the diagnosis of diseases of the intestinal lining, such as bacterial infections that cause diarrhea and malabsorption of nutrients
  • To diagnose diseases of the small intestines. Your doctor may suggest this for you if you have already gotten an x-ray and received abnormal results, if you have otherwise unexplained diarrhea or gastrointestinal bleeding or if you have tumors in your small intestine.

Who Performs It

  • A physician who is trained in endoscopic procedures

Special Concerns

  • Although small bowel biopsy may provoke some anxiety and cause slight discomfort, it is not painful and complications are rare.
  • Small bowel biopsy may not be safe in people with certain bleeding disorders. Blood coagulation studies may be performed to ensure you are a proper candidate for the procedure.

Before the Small Bowel Biopsy

  • Do not eat or drink anything for at least 4 hours before the test.
  • Inform your doctor if you regularly take anticoagulants or nonsteroidal anti-inflammatory drugs (such as aspirin, ibuprofen, or naproxen). These medications must be discontinued for some time before the test to reduce the risk of bleeding complications.

What You Experience

  • You will begin the test sitting up on a table.
  • A local anesthetic (such as lidocaine) is sprayed onto the back of your throat to suppress the gag reflex as the capsule and tube are inserted.
  • The doctor inserts the lubricated capsule and tube into your throat and then asks you to flex your neck and swallow to aid in the advancement of the tube down through your esophagus.
  • You will not be able to speak when the tube is inserted, but your breathing will not be affected.
  • Next, you will lie on your right side as the doctor advances the capsule and tube into your stomach, through the pylorus (the opening of the stomach into the small intestine), and finally into the small intestine. Continuous x-ray imaging, or fluoroscopy, is used to guide the progress and positioning of the device.
  • When the capsule is in the proper position, you will be asked to roll onto your back so that the doctor can verify the capsuleā€™s placement using fluoroscopy.
  • To obtain the biopsy sample, a syringe is attached to the outer end of the tube and suction is applied. The suction draws a small piece of tissue into the capsule and then closes off the capsule, which cuts off the tissue from the intestinal lining.
  • The tube is slowly withdrawn, and the tissue sample is sent to a laboratory for analysis.
  • The procedure lasts 45 to 60 minutes.

Risks and Complications

  • When performed by a skilled professional, small bowel biopsy is typically safe and well-tolerated.
  • Rare but serious complications of this procedure include bleeding, blood infection, and perforation of the bowel (which requires surgical repair).

After the Small Bowel Biopsy

  • You may leave the testing facility promptly after the test is completed.
  • Do not eat or drink anything until your gag reflex returns, usually in a few hours. (Touching the back of the throat with a tongue depressor tests for this reflex.)
  • You may have black, tarry stools due to bleeding for a short period of time.
  • Contact your doctor immediately if you develop a fever or abdominal pain.


  • Biopsy specimens are sent to a pathology laboratory and examined under a microscope for changes that indicate a bacterial or parasitic infection or another abnormality.
  • This test usually results in a definitive diagnosis. Your doctor will recommend an appropriate course of treatment, depending on the specific problem.


The Johns Hopkins Consumer Guide to Medical Tests

Simeon Margolis, M.D., Ph.D., Medical Editor

Updated by Remedy Health Media

Publication Review By: the Editorial Staff at

Published: 23 Jan 2012

Last Modified: 11 Sep 2015