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    Gastrointestinal endoscopic biopsy


    Biopsies are commonly taken during endoscopic investigation of gastrointestinal lesions and inflammatory conditions.1-9 There is conflicting evidence as to the benefit of biopsy of mucosa that appears normal endoscopically.10,11

    This protocol is also applicable to other small biopsies taken during gastrointestinal procedures such as peritoneal biopsies.

    Record the patient identifying information and any clinical information supplied together with the specimen description as designated on the container. See overview page for more detail on identification principles.

    Important information to include:10

    • Oesophagus –presence of Barrett’s oesophagus, site of biopsies, previous history
    • Gastric –Helicobacter pylori history, other test results
    • Colorectal –Note if biopsy is follow up of bowel cancer screening program result

    Follow best practice procedures to minimise cross over contamination of small fragments to other specimens.12

    See general information for more detail on specimen handling procedures.

    Inspect the specimen and dictate a macroscopic description.

    External Inspection

    Describe the following features of the specimen:

    Number of pieces

    • Record the number of pieces of tissue present. Multiple” should only be used to describe specimens where biopsies are too numerous to count.


    • Tan
    • Red
    • Yellow
    • White


    If discernable see colorectal polyp

    • Sessile
    • Pedunculated

    The appearance of fragments can be indicative of the type of tissue present:1

    • Tan and firm -usual tissue appearance
    • Yellow and soft -adipose tissue
    • Red and friable -haemorrhagic tissue or blood clot that may not survive processing
    • Brown and hard -possible foreign body e.g. seeds that may be difficult to cut on microtome

    Specimen size (mm)

    • Each fragment in three dimensions

    Where multiple fragments are present, the range of maximum sizes may be appropriate.


    Not required.

    Internal Inspection

    Not required.


    Submit all tissue. Transfer directly into cassettes for processing. Biopsy pads, lens paper or similar are required to prevent loss of tissue during processing.13

    Generally biopsies will be received without orientation but if received on a strip of material suitable for processing, transfer as received to a cassette. This will allow embedding on edge into block to demonstrate mucosa and submucosa in microscope sections.10

    Where biopsies from multiple sites are received, ensure that specimens from each site are processed in separate cassettes and identified in the block allocation key.10

    Record details of each cassette.

    An illustrated block key similar to the one below may be useful.

    Block allocation key

    Cassette id
    No. of pieces


    Dr Ian Brown for his contribution in reviewing and editing this protocol.


    1. Lester SC. Small Biopsies. In: Manual of Surgical Pathology, Saunders Elsevier, Philadelphia, 2010;243-245.
    2. Holscher AH, Vallbohmer D and Bollschweiler E. Early Barrett's carcinoma of the esophagus. Ann Thorac Cardiovasc Surg 2008;14(6):347-354.
    3. Miehlke S, Hackelsberger A, Meining A, Hatz R, Lehn N, Malfertheiner P, Stolte M and Bayerdorffer E. Severe expression of corpus gastritis is characteristic in gastric cancer patients infected with Helicobacter pylori. Br J Cancer 1998;78(2):263-266.
    4. Vannella L, Lahner E and Annibale B. Risk for gastric neoplasias in patients with chronic atrophic gastritis: A critical reappraisal. World J Gastroenterol 2012;18(12):1279-1285.
    5. Geraghty JM and Talbot IC. Diversion colitis: histological features in the colon and rectum after defunctioning colostomy. Gut 1991;32(9):1020-1023.
    6. Lanza G, Messerini L, Gafà R and Risio M. Colorectal tumors: The histology report. Digestive and Liver Disease 2011;43:S344-S355.
    7. Muto T, Bussey HJ and Morson BC. The evolution of cancer of the colon and rectum. Cancer 1975;36(6):2251-2270.
    8. Kleer CG and Appelman HD. Ulcerative colitis: patterns of involvement in colorectal biopsies and changes with time. Am J Surg Pathol 1998;22(8):983-989.
    9. Guindi M and Riddell RH. Indeterminate colitis. J Clin Pathol 2004; 57(12):1233-1244.
    10. Feakins R, Campbell F, Mears L, Moffat C, Scott N and Allen D. Tissue pathways for gastrointestinal and pancreatobiliary pathology, The Royal College of Pathologists, London, 2009.
    11. Howat A, Boyd K, Jeffrey M, Lessells A, Shepherd NA and McCluggage G. Histopathology and cytopathology of limited or no clinical value, The Royal College of Pathologists, London, 2005.
    12. Lester SC. Extraneous Tissue. In: Manual of Surgical Pathology, Saunders Elsevier, Philadelphia, 2010;33-34.
    13. Ibrahim NB. ACP. Best Practice No 155. Guidelines for handling oesophageal biopsies and resection specimens and their reporting. J Clin Pathol 2000;53(2):89-94.

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      GI biopsy 1

      Random colonic biopsies

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      Terminal ileum biopsies

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      Small sessile polyp (tubular adenoma)

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