How best to obtain intestinal biopsies

Indications for intestinal biopsies can range from chronic vomiting and diarrhea to weight loss and even hypoproteinemia.

Indications for intestinal biopsies can range from chronic vomiting and diarrhea to weight loss and even hypoproteinemia. Other reasons include “negative” exploratory surgery or trying to explain why a patient keeps ingesting foreign bodies.


There are multiple techniques for obtaining intestinal biopsies in cats or dogs. The least invasive is endoscopy, although it needs to be performed under general anesthesia. A major benefit is it allows visualization of the esophagus, the stomach, and the proximal small intestine.

Seeing the patient’s mucosa can help with collecting more representative samples from specific lesions.
Endoscopic biopsy sites usually heal quickly with minimal complications (in the right hands). They can
be performed in patients who have low protein levels that would make them poor candidates for surgery.

Endoscopy may be a fairly quick and minimally invasive procedure, but it is not without the following shortcomings:

  • limitation to the proximal gastrointestinal tract (although colonoscopy also is possible);
  • depending on the patient’s size and the length of the endoscope, more or less of the intestinal length can be reached;
  • by definition, no visualization of other abdominal organs;
  • biopsies are not full-thickness since they only include the mucosa and submucosa. As lesions below the submucosa will be missed, some diseases, such as inflammatory bowel disease (IBD), may not be accurately diagnosed; and
  • the procedure requires a significant financial investment and some serious technical skills.


Most colleagues are comfortable performing a laparotomy, even though it is a more invasive way to obtain intestinal biopsies. Surgical biopsies allow you to take full-thickness samples of the intestines, which are necessary to diagnose some diseases. A laparotomy also allows other abdominal organs to be visualized, palpated, assessed, and biopsied.

If you face a “negative” exploratory, you can—and should—take biopsies of multiple other abdominal organs, what some call poetically a “biopsy buffet.” This can include biopsies of the liver, pancreas, lymph nodes, etc.

There are several techniques for collecting intestinal biopsies during a laparotomy, including wedge resection, modified wedge, and punch biopsy. All techniques allow harvesting full-thickness samples.

An important consideration is to start with the least contaminated area, then move to the next most contaminated site. Consider changing your scalpel blade and surgical instruments if contamination by bacteria or cancer cells is suspected. Let’s look at each technique more closely.

Wedge technique

This method is fairly straightforward. Isolate the area of intestine you will be sampling and surround it with moistened lap sponges. Milk lumen contents away from where your incision will be. An assistant can gently occlude the intestinal lumen with two fingers on each side of the proposed biopsy site.

Using an 11 or 15 scalpel blade, make a full-thickness stab incision through the antimesenteric intestinal wall. Create an elliptical wedge. Once your sample has been excised, place it delicately in a formalin-filled container. Avoid crushing the sample.

Biopsy sites can be closed using 5-0 to 3-0 suture material (e.g. polydioxanone) in a simple or ideally continuous pattern.
A Gambee pattern also can be used. All sutures should be appositional (i.e. not inverting, not everting, and not crushing). A single layer is sufficient.

In small patients, if stenosis is a concern, the incision can be made longitudinally, and the suture placed transversally. Biopsy sites should then be leak-tested like an enterotomy site to avoid complications such as dehiscence and peritonitis. In addition, they can be omentalized.

Wedge modification

A variation of the wedge technique uses a stay suture to help elevate the intestinal wall, allowing for an easier and hopefully smaller wedge resection. Your biopsy site should be prepared as described in the previous section Place a full-thickness 3-0 or 4-0 stay suture through the antimesenteric wall at the site you would like to sample. Attach both ends of the stay suture to a hemostat and gently lift it, thereby elevating the intestinal wall. With an 11 or 15 scalpel blade, make a full-thickness elliptical incision on both sides of the stay suture. Close as usual.

Punch biopsy

The third technique uses a Keyes skin biopsy punch. They are inexpensive, so use a new one for each patient to ensure sharp edges and neat biopsies. The size varies based on the patient, but 4 to 6 mm is typically adequate for sampling.

Your biopsy site should be prepared as described previously. Place a sterile (i.e. autoclaved) tongue depressor under the section of bowel you will be sampling. Gently place the punch on the antimesenteric aspect of the bowel. Apply slight downward pressure in a twisting motion until you have achieved a single full-thickness cut. Be very careful not to cut into the opposite side of the intestine (i.e. the one against the tongue depressor).

Occasionally, the biopsy sample will remain attached to the bowel. In that case, use scissors or a scalpel blade to free it up. Close the biopsy site as usual.

In any of these techniques, multiple samples should ideally be collected. At a minimum, in a typical “GI patient,” harvest biopsies from the stomach, the duodenum, the jejunum, and the ileum, this last area being very important. The distal end of the small intestine is often neglected, yet some lesions tend to be found in the ileum more than other regions.

Other techniques

There are other, less common options to biopsy the intestine.

  • A percutaneous, ultrasound-guided biopsy is one method to consider, although a fine-needle aspirate is more common.
  • “A very slick modification to guide your decision to biopsy specific areas of the intestine is the use of intraoperative ultrasound,” explains Eric Lindquist, BS, DMV (Italy), DABVP, owner of SonoPath, a mobile ultrasound and telemedicine company based in Sparta, N.J. “This technique allows the ultrasonographer to guide the surgeon to biopsy areas where the intramural intestinal architecture is altered. These lesions may otherwise not be visible to the naked eye. This ensures complete sampling of the most progressed pathology in the intestine.”
  • Intestinal biopsies also can be harvested through laparoscopy. There are limitations as far as which portions of the intestine can be reached and biopsied (the duodenum and ileum are tougher). There also are significant costs involved, and the learning curve is very steep.

For most general practitioners, the least complicated way to biopsy the intestine is to perform a laparotomy, allowing you to easily obtain answers to diagnose common findings such as IBD and cancer.

Phil Zeltzman, DVM, DACVS, CVJ, Fear Free Certified, is a board-certified veterinary surgeon and author. His traveling surgery practice takes him all over Eastern Pennsylvania and Western New Jersey. You can visit his websites at and
Kat Christman, a certified veterinary technician in Effort, Pa., contributed to this article.

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