Canine Fecal Analysis: What Can Your Dog’s Poop Reveal About Their Health?

Believe it or not, any wastes that come out of your dog’s body carry useful information.

Gross is in the eye of the beholder. Our dogs feel about poop quite differently than we do. To a dog, poop can be a source of intel, a snack, as well as sometimes a source of missing nutrients.

What can your veterinarian learn from your dog’s poop that you cannot on your own?

First, your veterinarian will take a look at it the same way you do—with their eyes—consistency, color, and things that don’t belong. There is a lot to be learned from that, but not everything can be seen with the naked eye.

Canine fecal analysis methods

Microscopic examination

Looking at a fecal sample under a microscope can reveal the presence of intestinal parasites such as roundworms, hookworms, whipworms, and even coccidia. With some luck, stool mixed with saline can show Giardia swimming around on the slide.

This test can help with a quick diagnosis, but only when positive. A negative test doesn’t automatically mean there aren’t any cooties, just that none of them made it on the slide.

Fecal Floatation

Fecal floatation is a bit more sophisticated, and it involves stool being mixed with a special fluid that causes parasite eggs to float to the surface. Again, it may be centrifuged first.

The eggs are then collected from the surface and examined under a microscope. This technique is more reliable.

Further reading: Fecal Flotation
Fecal Float (Fecal Flotation) Parasite Pictures Gallery

Baerman technique

Fecal floatation won’t detect parasites that pass larvae rather than eggs. So that’s where this technique comes in. It is pretty much the opposite of floatation–the goal is to get the larvae to make their way to the bottom of a special funnel used for this test.

Baerman technique is most commonly done to detect lungworm.

Why would you examine poop for a worm that lives in the lungs? As this infection causes a cough,  eggs get coughed up and swallowed, making their way to the intestine.

Further reading: Fecal Baermann

Fecal Gram Stain

This form of fecal cytology uses a stain substance to highlight certain things under the microscope. It can be used to look for abnormal yeasts and bacteria. As much fun as this is, it seems to be a controversial and outdated approach. Its primary use is to identify Clostridia. But there are many species, some of them harmful and some of them not, and many other bacteria can look alike. It’s all fine and dandy unless it leads to wrong conclusions.

Further reading: Canine fecal analysis: Gram Stain Protocol

Fecal culture

If you really want to know what bacteria is present in your dog’s poop, help it grow. Which is what this test is. The bacteria in the small sample is nurtured and nourished, so they multiply, making it easier to see what they are. The problem is that there are so many normal bacteria in the digestive tract that you’ll have all sorts of things growing. It can, however, sometimes be helpful when looking for campylobacter, salmonella, or clostridia.

ELISA testing

Here is where it gets fancy. ELISA is a form of immunology testing. It is used to diagnose all sorts of infections; when it comes to poop, it can detect things like parvovirus, Giardia, or whipworm. It is highly sensitive and will discover things other tests might miss.

Further reading: Fecal Dx antigen testing

SNAP Assay

SNAP assay is ELISA testing packaged for convenience. Instead of having to send a sample to a lab and waiting for the results, your veterinarian can perform this test right on the spot in the clinic.

Further reading: SNAP Giardia Test

Fecal panels

If you think immunology testing is fancy, how about detecting cooties by looking for their DNA? Unlike ELISA testing, it doesn’t need antibodies that may not be present yet or, if the immune system doesn’t respond, might never be there. But, like with everything, it has its downside. If any one test were perfect, there would only be one test.

For example, you might end up with all sorts of results, but does that mean there is actually a problem? False positives are common. Unless you’re looking to confirm something, in particular, this testing is more likely to be more confusing than useful. On the other hand, this test is actually less sensitive than ELISA when looking for Giardia.

Further reading: RealPCR testing

Canine fecal analysis methods overview

Method	Description	How Performed	What It Detects	Limitations/Notes
Microscopic Examination	Basic visual check under a microscope for parasites.	Stool mixed with saline and viewed directly.	Protozoa like Giardia, some eggs.	Less reliable; misses many parasites without concentration.
Fecal Floatation	Concentrates parasites by making eggs float.	Stool mixed with dense fluid (e.g., sugar/salt solution), centrifuged; surface skimmed for microscopy.	Parasite eggs (roundworms, hookworms, whipworms, coccidia).	Common and effective; misses larvae or non-floating parasites like Giardia (needs special solutions).
Baermann Technique	Specialized for larvae detection.	Stool in warm water funnel; larvae sink to bottom for collection.	Larvae from lungworms or other infections.	Used when floatation fails; detects coughed-up/swallowed larvae in stool.
Fecal Gram Stain	Stains to highlight microbes.	Stain applied to smear; viewed under microscope.	Yeasts, bacteria (e.g., Clostridia spores).	Controversial—overestimates Clostridia due to look-alikes; not definitive for diagnosis.
Fecal Culture	Grows pathogens in lab.	Stool plated on nutrient medium; incubated for growth.	Bacteria like Campylobacter, Salmonella.	Time-consuming; normal gut bacteria can obscure results.
ELISA Testing	Immunological antigen detection.	Sample tested for specific proteins.	Viruses (parvovirus), parasites (Giardia, whipworms).	Highly sensitive; quick but can miss low-level infections.
SNAP Assay	On-site ELISA variant.	Quick kit test in clinic.	Similar to ELISA (e.g., Giardia, parvovirus).	Convenient for immediate results; reliable for common issues.
Fecal Panels	DNA-based screening.	PCR or similar to detect genetic material.	Multiple parasites/infections at once.	False positives possible; less sensitive for some like Giardia.
Future Microflora Analysis	Emerging non-invasive gut biome testing.	Analyzes bacterial balance in stool.	Potential IBD or dysbiosis indicators.	Research stage; could replace invasive biopsies for chronic gut issues.

The future of canine fecal analysis?

Work is being done testing whether evaluating gut microflora could be used to diagnose inflammatory bowel disease (IBD). So far, the results seem promising. This would be a significant advantage because so far, the only way to diagnose IBD conclusively is via biopsy.

Who knows what other useful information we might discover in our dogs’ poop.

Beyond canine fecal analysis: genetic testing

Genetic testing is available for conditions related to EPI (Exocrine Pancreatic Insufficiency) in dogs, particularly for hereditary cobalamin (vitamin B12) malabsorption, which is often linked to or secondary to EPI.

This disorder impairs B12 absorption in the intestines and can mimic or complicate EPI symptoms, including weight loss, diarrhea, and malabsorption. It’s caused by mutations in genes such as CUBN or AMN, and testing can identify carriers, affected dogs, or unaffected dogs.

Commonly affected breeds

This disorder is primarily heritable in Border Collies, Australian Shepherds, Beagles, Giant Schnauzers, Shar-Peis, and Komondors. For example, in Border Collies, it’s associated with a CUBN mutation; in Komondors, with an AMN variant.

Further reading: Imerslund-Gräsbeck Syndrome (IGS)

There is ongoing research into the heritability of EPI, particularly in GSDs, but diagnosis relies on blood tests such as cTLI (canine trypsin-like immunoreactivity), rather than genetics.

Related articles:
My Dog’s Poop: What Can You Learn from Your Dog’s Stool

Further reading:
Why Does My Veterinarian Want a Poop Sample?