GI Biopsies & EMRs

Auto Text: “Insert _ Bit Biopsy” (fill in blank with # of containers received, up to 10) or “Insert EMR”


Gastrointestinal biopsies should arrive in the surgical pathology laboratory in fixative (formalin). If they arrive fresh and are for routine histopathology, please add formalin to begin the fixation process.

Orientation of Large Polyps (PA ONLY SPECIMENS): It is critical that polyps be cut longitudinally so that the surgical margin can be evaluated. Any identifiable margin (cauterized) tissue should be inked. Polyps are sometimes impaled on a needle that marks the long axis.

Endoscopic mucosal resections (PA ONLY SPECIMENS): General guidelines include a gross photograph and consult from the attending pathologist. For intact specimens, the tips need to be submitted separately. The lateral and deep margins should be inked. Orienting stitches may be present. If so, the number and specificity of any stitch orientation will guide how many inks are to be used. Serially section and submit the the specimen sequentially and entirely (tips separate and designated; refer to pathologist for en face vs. perpendicular sections).


The following points should be kept in mind when processing this material:

  1. In the clinical history, record the pertinent endoscopic findings found in the accompanying endoscopy report.  Include the clinical history and indication for the procedure, endoscopic findings (gross appearance/lesions), and a summary of the impression. Exclude extraneous information (how the biopsy was taken, evidence of bleeding, mechanics of the procedure, treatment/follow-up recommendations).  Please do not dictate the report verbatim but succinctly summarize it with accuracy.
  2. Dictate the patients’ age and sex into the clinical history.
  3. If the requisition states the biopsy was taken for molecular markers, confirm the protocol is “Biopsy for Molecular Testing” and there is a white cassette for the tissue getting one level only cut in histology.  Submit all bits of tissue in mesh bag in one cassette.
  4. Words/phrases NOT to include: severe/moderate/mild inflammation characterized by, no bleeding or stigmata of recent bleeding, was found, localized/diffuse, evidence of a prior, flexible or pediatric (in reference to colonoscopy), mucosal changes characterized by, no stated history, screening for colorectal neoplasm, no pertinent findings.
  5. Include: family or personal history of colorectal cancer or colonic polyps
  6. If there were no endoscopic findings, simply state ‘There entire exam was normal”.
  7. State the number, size and location of colon polyps.
  8. Note if any polyp was NOT retreived.
  9. If an EMR or ESD was performed, please note the procedure performed. No procedure is needed for normal polyps.
  10. When starting a sentence with a numeral, it should be the word not the number: Ex. Two polyps were found.
  11. Always check the lid, all sides of the Millipore paper, and the container bottom for biopsies.
  12. For upper endoscopic procedures, the parts should be accessioned and submitted in sequence from proximal to distal: 1. Esophagus, 2. GE junction, 3. Cardia, 4. Gastric body, 5. Gastric antrum, 6. Duodenum.
  13. For colonoscopic procedures the parts should be accessioned and submitted in sequence from proximal to distal: 1. Terminal ileum, 2. Cecum, 3. Ascending, 4. Hepatic flexure, 5. Transverse, 6. Splenic flexure, 7. Descending, 8. Sigmoid, 9. Rectum.
  14. For each part, record the number of biopsies in each container and the range in maximal dimension  (e.g. four fragments of tissue, ranging from 0.1 to 0.3 cm in greatest dimension).
  15. NO MORE THAN THREE (3) biopsies should be placed in each cassette, between two blue sponges. Additional pieces can be submitted in cases of fragmented adenoma, where orientation is not crucial.
  16. The specimen should be submitted entirely.

Updated on 11/15/22 SRR

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