Chronic diarrhea in horses can be a frustrating, elusive challenge for owners and veterinarians alike. Typically characterized by the continuous or intermittent passage of soft, watery feces, diarrhea can be linked to underlying colonic abnormalities that lead to intermittent colic (abdominal pain) and an overall decline in body condition, health, and welfare.

Amy Stewart, DVM, PhD, Dipl. ACVIM-LA, assistant teaching professor at the North Carolina State University College of Veterinary Medicine, in Raleigh, reviewed the most up-to-date guidelines for investigating equine diarrhea cases at the 2026 Veterinary Meeting and Expo, held Jan. 17-21, in Orlando, Florida.

Chronic Diarrhea in Horses: What It Is, and What It Isn’t

Stewart established that clinical signs of diarrhea in horses vary widely, from a feces-stained, dirty tail to intermittent colic, sudden weight loss, or periods of reduced appetite. “Evaluating severity can be difficult, as the equine colon’s efficient water resorption can mask ongoing disease,” she said. “I recommend investigating all possible causes rather than assuming a benign ‘fecal water syndrome’ (FWS), particularly if there are additional signs of ill health.”

Fecal Water Syndrome and The Role of the Microbiome

“Fecal water syndrome affects apparently healthy horses that exhibit intermittent leakage of water before, sometimes during, and/or after passing otherwise normal feces,” Stewart explained.

Researchers have highlighted the complexity of the equine gut microbiome; both disease and medication can disrupt microbial populations therein, potentially leading to persistent FWS. However, they do not yet know a definitive cause. Additional factors associated with FWS might include stress, dietary imbalance, or types of fiber in the diet. To diagnose fecal water syndrome, Stewart said veterinarians must first exclude underlying causes of true diarrhea.

Causes of Diarrhea in Horses

Diarrhea in horses can be infectious or noninfectious. Common infectious causes include internal parasites—most commonly cyathostomes (small strongyles)—and bacteria such as Salmonella and Clostridium difficile.

“Diagnosing parasitism can be especially challenging when parasites encyst within the colon wall; fecal egg counts (FEC) may not reflect true parasite load,” Stewart said. “And while advanced tests, including serum ELISA for strongyles, show promise, they are not yet standard in the U.S.”

She added that bacterial causes, particularly in chronic Salmonella carriers, can also be difficult to pinpoint due to intermittent and low-level shedding. “Diagnosis often requires repeated or pooled fecal samples and, occasionally, culture of a rectal biopsy,” she said. “Treatment is complicated as antibiotics can prolong shedding. Clostridium-associated diarrhea is most often recognized after antibiotics disrupt normal flora, and diagnosis requires toxin identification.”

Noninfectious causes of diarrhea include sand ingestion and various inflammatory or infiltrative bowel diseases, including lymphocytic plasmacytic enteritis/colitis (a rare infiltrative intestinal disease) or neoplasia (abnormal tissue growth) such as lymphoma.

Veterinarians and researchers recognize long-term non-steroidal anti-inflammatory (NSAID) administration as a cause of right dorsal colitis, commonly manifesting as low blood protein with few external signs. Stewart noted that while foals might experience diarrhea caused by issues in the small intestine, chronic disease of the large intestine is the most common culprit in adults.

Current Diagnostic Options and Limitations

With idiopathic diarrhea cases Stewart follows a progressive diagnostic strategy. She starts with taking a comprehensive history, conducting a thorough physical examination, and running laboratory tests that include blood panels, FEC, and Salmonella testing.

If initial assessments are inconclusive, her next steps include an abdominal ultrasound, radiographs, abdominocentesis (collection of peritoneal fluid), and rectal mucosal biopsies. “The latter is valuable for differentiating inflammatory from neoplastic conditions, while imaging assesses for conditions such as sand accumulation via radiographs or colonic wall thickening via ultrasound,” she said.

Managing Horses with Chronic Diarrhea

Successfully managing chronic diarrhea in horses depends on identifying and addressing the underlying cause. Stewart emphasized the importance of dietary management and carefully reviewing all feed and supplements for potential allergens that could irritate the gut.

For confirmed moderate-to-severe infiltrative bowel diseases, whether inflammatory or neoplastic, veterinarians might recommend immunosuppressive therapies such as steroids. Cases linked to sand ingestion require effective psyllium regimens, while infectious cases call for strict biosecurity and, occasionally, antimicrobial therapy.

Take-Home Message

In all cases of diarrhea in horses, Stewart stressed the importance of ruling out treatable infectious or noninfectious causes of diarrhea before diagnosing a particular patient with the less serious condition fecal water syndrome.