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Intestinal Biopsy - the ongoing discussion

When it comes to discussing intestinal biopsies, the same question seems to be asked over and over again: "Do I need full thickness or partial thickness biopsies to get a diagnosis"? While working in general practice I asked this question of many Pathologists and Internists. The answer was as variable as the personalities the question was being posed to. At times the opinion would be that full thickness biopsies were really the only way to confidently differentiate between diseases that can look similar (think Inflammatory Bowel Disease vs. Lymphoma). Just as quickly as that seemed to be "gospel", the opinions would change and partial thickness biopsies were now the best (and least invasive) option. So the question remains - what's better? While it is important to remember that I am a general practitioner and not a specialist, I feel it is still valid for me to present the most logical approach I take when veterinarians call me asking for biopsies.

First of all, I think it is important to appreciate that obtaining biopsy samples (in general) is best done in the least invasive way possible. A faster, less painful recovery is obviously better for the animal in question, but will also help the pet owner more readily accept the treatment recommendations. When a veterinarian calls me asking for intestinal biopsies, I explain the 2 methods I can use to help:

1. Flexible endoscopy involves passing a long flexible scope along the gastrointestinal tract in order to visualize from within. This scope can be passed through the mouth, down the throat and into the stomach and first part of the small intestine. Conversely, it can also be passed into the colon and up through the large intestine and (in some cases) into the last portion of the small intestine. When performing flexible endoscopy the biopsy samples are collected with a long biopsy forcep that is passed through the scope. These samples are called "partial thickness" because they only sample the innermost layers of the wall of the intestine.

2. Rigid endoscopy: By contrast, "full thickness" biopsies can be collected by taking samples that demonstrate all of the layers of the intestinal wall. In order to collect these samples in a minimally invasive way, a small incision is made into the abdomen and laparoscopy is performed. The intestine is grasped and brought through a small incision to allow sample collection and sutures (stitches) to be placed into the intestine to repair the defect left after the biopsy. In the past, collecting full thickness biopsies would require a larger abdominal incision and many pet owners were hesitant to put their per through this. With the use of laparoscopy, the abdominal incision is much smaller allowing for faster recovery.

So Which Is Better?

A general agreement seems to be that both full thickness and partial thickness biopsies are useful in diagnosing the majority of gastrointestinal diseases found in dogs and cats. The quality of the biopsy samples has (and always will be) the most important aspect of achieving a reliable diagnosis. However, in my opinion the decision to perform full thickness vs. partial thickness biopsies varies depending on the animal and the suspected disease. If a full representation of the small intestine is required (or wanted by the veterinarian), it can often make more sense to collect full thickness biopsies via laparoscopy. Flexible endoscopy is no doubt less invasive in comparison, but is also limited in how far into the small intestine the scope can be passed (thereby providing no guarantee of jejunum samples). In order to obtain samples from the Ileum (last segment of the small intestine) a colonoscopy must be performed (due to the extraordinary length of the small intestine). While this is certainly possible, it can be difficult to access all areas of the small intestine in smaller dogs and some cats. In addition, colonoscopy requires considerable patient preparation before performing the procedure (cleaning out the colon, etc).


When performed using minimally invasive techniques, both full thickness and partial thickness biopsies can be extremely helpful in obtaining a diagnosis. The choice between technique is best tailored to the individual patient and expectations and/or requirements of the clinician responsible for the case. Understanding the pros and cons of each approach can help ensure that our patients receive the care they need with the least amount of discomfort possible.

I am always happy to discuss potential cases with veterinarians to help determine the best approach. Please feel free to contact me.

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