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Approach to stool microscopy

Danny A Milner, Jr, MD, MSc(Epi)
Section Editor
Edward T Ryan, MD, DTMH
Deputy Editor
Elinor L Baron, MD, DTMH


Stool microscopy is a diagnostic tool for identification of parasitic organisms including protozoa and helminths; it is also useful for quantification of fecal leukocytes.

Issues related to stool microscopy will be reviewed here; clinical issues related to evaluation of patients with gastrointestinal symptoms are discussed separately. (See related topics.)


Analysis of stool for parasites has its highest clinical utility when caring for patients with diarrhea or intestinal symptomatology lasting two weeks or longer or during outbreaks of intestinal infection. Most intestinal infections resolve within a few days of onset, and microscopic evaluation of stool for parasites in such short-term enteritis is usually unrevealing.

The approach to organism identification via stool microscopy should be guided by the clinical presentation, including geographic exposure, age, and nature of clinical symptoms. The differential diagnosis of intestinal parasitic infection also includes bacterial and viral pathogens; in such cases, useful diagnostic tests include culture, antigen detection, fecal leukocyte count, serology, and/or specialized testing for viral pathogens. (See "Approach to the adult with acute diarrhea in resource-rich settings", section on 'Evaluation'.)

Rapid antigen testing is more useful than microscopy for diagnosis of Giardia, Cryptosporidium, and Entamoeba infection. In general, the presence of diarrhea that is watery and nonbloody that occurs in association with camping, animal contact, an outbreak, and/or HIV infection should prompt consideration of these organisms [1].

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Literature review current through: Oct 2017. | This topic last updated: May 04, 2017.
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