Horse diarrhea has dozens of possible causes, ranging from a simple feed change to life-threatening infections. The most common triggers in adult horses are parasites, bacterial infections, sand ingestion, stress, dietary shifts, and antibiotic use. Figuring out which one is affecting your horse depends on how suddenly the diarrhea appeared, how sick the horse seems overall, and what’s changed recently in its environment or routine.
Infectious Causes
Several bacteria and viruses can cause acute, watery diarrhea that comes on fast and often brings fever with it. The major players are Salmonella, two species of Clostridium (C. difficile and C. perfringens), Neorickettsia risticii (the organism behind Potomac horse fever), and equine coronavirus. Coronavirus typically also causes loss of appetite, lethargy, and fever. Salmonella and Clostridium infections can produce profuse, foul-smelling diarrhea, sometimes with blood, and can spread between horses sharing water sources, stalls, or pastures.
Infectious diarrhea tends to hit hard and fast. If your horse went from normal to severely loose stool within 12 to 24 hours, especially with a temperature above 101.5°F, an infectious cause is high on the list. These cases often need veterinary intervention quickly because horses lose enormous volumes of fluid and electrolytes through watery stool and can become dangerously dehydrated within a day.
Parasites and Larval Cyathostominosis
Small strongyles (cyathostomes) are one of the most common parasites in horses and a frequent cause of diarrhea, particularly in young horses between one and three years old. These parasites burrow into the lining of the large intestine during their larval stage and encyst there, sometimes for months. The real damage happens when huge numbers of larvae emerge from the gut wall all at once, causing sudden inflammation, diarrhea, weight loss, and sometimes colic.
This mass emergence is most common in winter and spring. Paradoxically, it can also be triggered by deworming. When a dewormer kills the adult worms living in the gut lumen, it can prompt the encysted larvae to emerge, creating a wave of intestinal damage. This is why a horse that was just dewormed sometimes develops diarrhea shortly afterward, and it’s a reason your vet may recommend a specific deworming strategy based on fecal egg counts rather than a blanket schedule.
Sand Accumulation
Horses that live on sandy soil or eat hay off the ground in sandy areas gradually swallow grit with every meal. Over time, sand accumulates in the large colon, where it irritates the intestinal lining and causes chronic or intermittent diarrhea, weight loss, and colic. You can sometimes hear a gritty, scratching sound if you press a stethoscope against the lowest part of your horse’s belly.
A simple test you can do at home: drop a few fecal balls into a plastic bag or rubber glove, add water, mix it up, and let it settle. If you see a layer of sand or grit at the bottom, your horse is ingesting significant amounts. Feeding hay in rubber mats or raised feeders, and using psyllium supplements on a regular schedule, can help move sand through the gut before it builds up to dangerous levels.
Antibiotic-Induced Diarrhea
Horses rely on a massive population of bacteria in their hindgut to ferment fiber and produce energy. Antibiotics don’t just kill the targeted infection; they disrupt this entire microbial community. Virtually all clinically relevant antibiotic classes can potentially cause colitis or diarrhea in horses. Research has shown that oxytetracycline, ceftiofur, and trimethoprim-sulfadiazine are all associated with diarrhea, though any antibiotic carries some risk.
What happens is that the normal, beneficial bacteria get suppressed, allowing harmful organisms like C. perfringens to multiply unchecked. If your horse developed diarrhea during or shortly after a course of antibiotics, this disruption of gut flora is the likely cause. Mild cases may resolve once the antibiotic course ends, but severe antibiotic-associated colitis can be dangerous and needs veterinary attention.
Diet Changes and Stress
The equine hindgut needs time to adjust to any dietary shift. Switching hay types, introducing grain, increasing the amount of concentrate feed, or turning a horse out on lush spring pasture can all overwhelm the microbial balance in the cecum and colon, producing soft stool or outright diarrhea. The general rule is to make any feed change gradually over seven to ten days.
Stress is another underappreciated trigger. Trailering, competition, changes in herd dynamics, or a move to a new barn can cause what’s sometimes called “stress colitis.” The mechanism involves changes in gut motility and blood flow to the intestines. This type of diarrhea is usually self-limiting once the stressor passes, but prolonged stress can lead to chronic loose stool and weight loss.
Toxins and Blister Beetles
Blister beetles produce a chemical called cantharidin that is extremely toxic to horses. These insects sometimes get trapped in alfalfa hay during harvesting, and even a few crushed beetles in a flake of hay can cause severe illness. Cantharidin is a potent irritant that damages the lining of the gastrointestinal tract and urinary tract, causing blistering and ulceration from the esophagus through the stomach and intestines.
Affected horses typically show signs of colic first: restlessness, sweating, elevated heart rate, and rapid breathing. Diarrhea, muscle tremors, and frequent painful attempts to urinate follow. One telltale behavior is that horses with cantharidin poisoning may dunk their muzzles into water troughs or appear to play in water, likely because of mouth and throat irritation. Severe cases can cause shock and death. This is a true emergency, and the prognosis depends heavily on how much cantharidin was consumed.
Inflammatory Bowel Disease
When diarrhea persists for weeks or months without an obvious infectious or dietary explanation, inflammatory bowel disease becomes a consideration. Equine IBD involves chronic inflammation of the intestinal wall that interferes with nutrient absorption. The small intestine’s ability to absorb sugars and other nutrients declines as the intestinal lining becomes damaged and thickened. Horses with IBD often lose weight steadily despite eating well, develop a poor coat, and may have intermittent or persistent loose stool.
Diagnosis is challenging. Ultrasound can reveal thickened bowel walls or enlarged lymph nodes in the abdomen, but a definitive diagnosis sometimes requires a biopsy obtained during surgery. Several forms of IBD exist in horses, including one involving clusters of inflammatory cells and blood vessel damage within the gut wall. Treatment typically involves long-term management rather than a cure.
How to Assess Severity at Home
Before your vet arrives, checking a few vital signs helps determine how urgent the situation is. A healthy adult horse at rest has a heart rate of 28 to 44 beats per minute, a rectal temperature between 99°F and 101.5°F, and a capillary refill time of one to two seconds (press a finger against the gum above the teeth, release, and count how quickly the pink color returns).
You can also estimate dehydration by checking the gums and skin. If the gums feel slightly dry but the skin still snaps back normally and the eyes look moist, the horse is roughly 4 to 5 percent dehydrated. That translates to about 20 to 25 liters of fluid deficit in a 500-kilogram horse (roughly 5 to 6 gallons). Dry gums combined with skin that stays tented when you pinch it on the neck suggests 6 to 7 percent dehydration or worse, and at that level most horses need intravenous fluids.
What Diagnostic Testing Looks Like
When a vet investigates equine diarrhea, the starting point is usually a fecal sample. A standard diarrhea panel includes aerobic bacterial culture to look for Salmonella, specific cultures and toxin testing for both C. perfringens and C. difficile, and a fecal float to check for parasite eggs. Some panels also screen for additional organisms like Rhodococcus equi in foals. Viral testing for rotavirus or coronavirus is typically run separately if the initial panel comes back negative.
For chronic cases, bloodwork can reveal protein loss and signs of malabsorption. Abdominal ultrasound helps evaluate the intestinal wall and surrounding lymph nodes. In areas where sand colic is common, abdominal X-rays can confirm sand buildup in the colon. The diagnostic path your vet chooses depends largely on whether the diarrhea is acute or chronic, how sick the horse is, and what risk factors are present in your area and management setup.