Chronic diarrhea in horses can be frustrating for owners and veterinarians alike, especially when the underlying cause isn’t immediately clear. Amy Stewart, DVM, PhD, Dipl. ACVIM-LA, assistant teaching professor at the North Carolina State University College of Veterinary Medicine, in Raleigh, highlighted notable case studies and provided practical guidelines for managing this common condition at the 2026 Veterinary Meeting and Expo, held Jan. 17-21, in Orlando, Florida.

Defining Diarrhea in Horses

Often defined as loose feces persisting for more than a week, chronic diarrhea in horses is usually linked to conditions of the large intestine (cecum, large colon, and small colon). Stewart pointed out that not everything that looks like diarrhea is pathologic (reflecting underlying disease). “Fecal water syndrome, (FWS), in which horses excrete water along with normal-appearing bowel movements, has less serious health and welfare implications than true chronic diarrhea,” she said.

Systematic Approach to Diagnosis

Stewart explained that she generally starts with history and diet evaluation, fecal diagnostics, and noninvasive management approaches, which typically include dietary modification and specific GI supplements such as probiotics. She then progresses to more invasive procedures, such as duodenal and rectal biopsies, if needed. “Endoscopy equipment is now widely available, making some of these diagnostics more accessible,” she said.

New Treatments for Diarrhea in Horses

Veterinarians consider fecal microbiota transplant (FMT) a promising, though not yet fully understood, intervention for severe or refractory chronic diarrhea cases, Stewart says. The emerging technique involves introducing healthy microbiota from a donor’s feces into the affected horse via nasogastric tube, but evidence in horses is limited and researchers are still working to determine optimal protocols.

Beyond FMT, Stewart described sand management, careful evaluation of supplements, and close dietary monitoring as foundational for managing diarrhea. “Steroids should be reserved for moderate to severe inflammatory cases, and all treatments must be carefully tailored to minimize risks, notably the debilitating hoof disease laminitis,” she said.

Notable Case Studies

Stewart shared four of her own cases to illustrate the complexity of chronic diarrhea and offered treatment protocols:

• A young gelding with a history of chronic diarrhea was diagnosed with sand enteropathy (intestinal disease) via abdominal radiographs and a large colon impaction on rectal palpation. She treated him using sand-clearing agents (psyllium) and supportive enteral fluids, resulting in improvement. Stewart stressed that the amount of psyllium recommended to treat cases of significant sand accumulation is often much larger than what is found in some supplements.
  
  
• An older gelding developed severe diarrhea after a change in hay and administration of the (rarely used) drug, clioquinol (iodochlorhydroxyquin), which has broad-spectrum antibacterial effects on the fecal microbiome. He suffered life-threatening colitis (inflammation of the large or small colon)—eventually traced to Salmonella—and needed intensive care, antibiotics due to extreme neutropenia (low white blood cell count), and an FMT to restore gut health.
  
  
• Another gelding dealt with what was presumed to be chronic FWS for more than two years. Diagnostics revealed mild inflammatory bowel disease, which responded best to dietary modification—removing long-stem forage and reducing unnecessary supplements.
  
  
• The final case involved a horse with persistent diarrhea that turned out to be gastrointestinal lymphoma, confirmed by rectal mucosal biopsy. While prognoses for horses with this condition are typically guarded, treatment options include immunosuppressive steroids and, in select cases, chemotherapy to enhance comfort and quality of life.

Take-Home Message

Chronic diarrhea can have many causes. Don’t jump to conclusions without a careful workup, Stewart said. As far as treatment, sometimes less is more. Simple diet modifications can be appropriate for nondistressed, otherwise-healthy horses with FWS. For true chronic diarrhea, newer therapies such as FMT offer hope for those managing particularly challenging cases.