The Scoop on Runny Poop: Diarrhea in Horses

Be it due to toxins, infectious agents, or simply diet changes, diarrhea in horses is no laughing matter.

It’’s a nasty, messy bodily (dys)function. And while it might be the source of little boys’ hysterical laughter and the stuff of snickers even among adults, it’s no joke to horse owners. Diarrhea occurs when the intestine doesn’t absorb electrolytes and water normally, instead allowing them to pass out of the body in loose or watery stools. It can be acute or chronic.

While some types of equine diarrhea present little to worry about if watched carefully, others can be life-threatening.

“In humans, diarrhea is generally benign,” says Rose Nolen-Walston, DVM, Dipl. ACVIM (LAIM), associate professor at the University of Pennsylvania’s New Bolton Center, in Kennett Square. “But horses have a rather delicate large intestine that has a very minutely balanced flora of bacteria, and something that disrupts that balance can cause diarrhea even without a particular pathogenic (disease-causing) bug being there. We call that colonic dysbiosis.”

What causes diarrhea, and why? What treatment options exist? When can you self-treat safely? At what point should you call your veterinarian? Can you expect a definitive diagnosis — or is a diagnosis even important? Read on for the definitive scoop on runny poop.

What Causes Diarrhea?

Diarrhea can originate from a wide array of conditions, some not even related to the digestive tract. Some horses develop mild diarrhea when their diet changes, and it’s not generally a big deal. But when toxins, sand, parasite larvae, and infectious agents such as bacteria and viruses get involved, it becomes a lot more serious.

Infectious Causes

Bacteria are one major source. Sometimes harmful bacteria enter the horse’s system; other times something upsets the balance of normally present bacteria, allowing “bad” bacteria to thrive and overtake the good.

Salmonella and Clostridium species are the most common bacterial offenders. Peter Heidmann, DVM, of Palm Beach Equine Clinic, in Wellington, Florida, says most Salmonella species are associated with livestock and birds. “The Salmonella species that affect cattle are the most pathogenic, and the secondary effects on the intestine on a microscopic level are very severe,” he says. “Those are the cases where horses get IV (intravenous) fluids and plasma for two to three weeks until their bowels start to heal.

“Horses can also carry Salmonella and not have any symptoms, so they can pass it to each other,” he adds. “If the healthy flora in the horse’s body is thrown off by even a small change in diet, or something bigger like a colic episode, or antibiotics, then Salmonella can grow up in its place.”

Clostridium difficile, which lives in the environment, also gets a foothold from gut flora imbalance, usually due to the horse having been treated with ­antibiotics for another infection. Fortunately, it responds to the antibiotic metronidazole.

Clostridium perfringens is a common cause of foal diarrhea. “Sometimes we’ll see it in very young foals, even in the first day or two of life, causing diarrhea and colic signs,” Nolen-Walston says. “We also see it in adult horses, especially in horses that have been treated with antibiotics.”

Neorickettsia risticii—the causative agent of Potomac horse fever (PHF)—are bacteria found in parasites that infect freshwater snails and caddisfly and mayfly larvae. For this reason, PHF is most common around bodies of water. Although originally isolated to the Potomac River area in Virginia and Maryland, Heidmann says Neorickettsia is endemic in other regions throughout the United States and recommends you talk to your veterinarian about its occurrence in your area. Vets commonly treat it with IV oxytetracycline or oral minocycline/doxycycline, antibiotics that are especially effective against neorickettsial organisms.

“These horses get very high fevers compared to other types of diarrhea,” Nolen-Walston says, “and although laminitis is always a very serious possible complication for any type of diarrhea, with Potomac horse fever you often see the laminitis before you even see the diarrhea.”

Coronavirus, which Nolen-Walston says is relatively newly described in horses, often occurs herdwide. Clinical signs can include a very high fever, mild diarrhea, and/or colic. Sometimes diarrhea is severe, with a very low white blood cell count.

“Coronavirus shreds the intestinal lining and can cause horses to become very sick,” Heidmann says. “The body has to reline the bowel, and it does so quickly, but it takes several days to more than a week, during which the horse may have severe diarrhea and secondary infections. Unlike bacterial infections, you can’t directly treat the organism, since there aren’t appropriate drugs to directly treat coronavirus in horses.”

Inflammation and Toxicity

Right dorsal colitis (inflammation of the right dorsal colon, or large intestine), aka non-steroidal anti-­inflammatory (NSAID) toxicity, can result from a particularly high dose or a reaction to an appropriate dose of NSAIDs such as phenylbutazone (Bute) or flunixin meglumine (Banamine). “The right dorsal colon becomes thickened and ulcerated, which can cause mild diarrhea and really low protein levels,” Nolen-Walston says.

Inflammatory bowel disease (IBD, which occurs when abnormal cells infiltrate the small intestine lining), as in humans, causes chronic diarrhea. And oleander and other plants toxic to horses can cause it, as well.

Gastrointestinal (GI) lymphoma is a cancer in which lymphocytes (a type of white blood cell) infiltrate the intestines. “Cases tend to be associated with less severe diarrhea that goes on for a longer time, and you’ll also see a chronic weight loss and low blood proteins,” Nolen-Walston says. “A newer blood test, TK1, can help distinguish this cause of diarrhea from IBD or other problems.”

Sand ingestion by horses eating off the ground is among the environmental causes of diarrhea. “Sand irritates the bowel lining and can cause damage from its weight as well as abrasion,” Heidmann says. “Clearing the sand by limiting further ingestion and potentially using psyllium to bind with the sand usually allows the bowel to re-establish a healthy lining.”

Parasitic Causes

Larval cyathostomiasis develops when small strongyle (cyathostomin) larvae burrow in the colon walls. A seasonal occurrence in late winter to early spring, they emerge all at once, causing the gut walls to leak protein-rich fluid and the horse to develop diarrhea and low blood protein. “It’s the larvae that cause disease, not adults,” Nolen-Walston says, “so doing a fecal egg count isn’t useful for diagnosis. There’s no correlation between the number of larvae and the number of egg-laying adults.

“Larval cyathostomiasis can only be diagnosed on necropsy (post-mortem exam) or biopsy (tissue removal for evaluation), so we treat it if we suspect it’s there based on the horse’s deworming history, age, and clinical signs,” she adds. “It’s frequently fatal, but very rare. The best treatment is moxidectin, which is the only dewormer that reliably kills the larvae.”

Causes in Foals

Foal-heat diarrhea is extremely common in the week or two following birth, Nolen-Walston says. “It seems to occur when the mare comes into foal heat, but no one knows what’s really causing it,” she says. “Those foals remain alert and eating well, and the diarrhea is mild. So if a foal owner sees that a foal has more watery fluid (than wet or liquid feces) or seems dull or has a fever, that’s not consistent with foal heat diarrhea, and they should call their veterinarian.”

Rhodococcus equi is an extremely common pathogen in foals, Nolen-Walston says, its main effect being lung abscesses. “About one-third of these cases involve disease outside the lungs, and diarrhea is one of the more common forms,” she says. “Rhodococcus is shed in feces, but foals can shed it even if they don’t have clinical disease. If we suspect Rhodococcus diarrhea, we’ll usually take a sample of fluids from the trachea to identify whether there’s Rhodococcus pneumonia in the lungs.”

Rotavirus is the most common viral cause of diarrhea in foals, especially foals one week to two months old. “It destroys the pits of the villi in the foal’s small intestine, so the foal doesn’t absorb its milk properly,” Nolen-Walston says. “(The foal) stops making lactase, the enzyme that digests milk, so in turn it causes the intestines to leak fluid from the body into the intestines, and the foal becomes dehydrated. The foal needs to be quarantined and PPE (personal protective equipment for handlers) and biosecurity employed.”

Self-Treat or Call in a Pro?

Sometimes self-treating is appropriate. “With the no-big-deal scenario of a change in feed—say, from grass hay to alfalfa—the horse may have loose stools (aka ‘cow plop’) but will still feel well,” says Heidmann. “But if it continues for 24 hours or more or if the horse is sick, we start to worry they’re losing water, protein, and electrolytes in their manure. Supportive care (your veterinarian administering IV fluids to rehydrate the horse, balancing electrolytes, giving plasma to replace protein lost through lack of absorption, and adjusting pH) can replace those things. And there are ways, even over the phone at 24 hours, that your veterinarian can say, ‘Okay, I think we’re safe to wait a day,’ or, ‘No, we really need to pull bloodwork now to see what’s going on.’ ”

“The most important thing to remember is that with horses, a couple things go on,” Nolen-Walston adds. “First, bacterial flora problems can become fatal. Intestines can become inflamed and bacterial toxins (endo- and exotoxins) can leak from the intestinal contents into the bloodstream, causing profound disease or even death, so any horse that has really watery diarrhea should be seen that day—particularly if the horse is dull, has reduced appetite, or its gums are red or purple rather than the normal pink.”

Diagnosis: Frequency & Importance

Nolen-Walston, who works up most of the diarrhea cases at New Bolton, says she isolates a specific pathogen in only about 50% of the cases she sees.

“The best testing,” Heidmann says, “is DNA using PCR (polymerase chain reaction testing). But even that has a high number of false negatives. It’s frustrating for both clients and veterinarians because sometimes a cause helps direct therapy. But in my practice most colitis patients receive nonspecific treatment with supportive care.

“It’s intellectually gratifying to the vet and emotionally satisfying to the client to know what the risk factors are for their horse for the future,” he adds, “but on a practical basis, we treat diarrhea pretty much the same based on symptoms rather than on the organism that might be there.”

In some cases, however, diagnosis is extremely important. “Some causes, like Salmonella, are highly contagious and can even become entrenched in a hospital environment, infecting other patients,” Nolen-Walston says. “So it can be important to rule out the contagious causes. Also, a few causes, such as PHF, call for a specific treatment that if not given is much more likely to result in fatality.”

Depending on a horse’s clinical signs, veterinarians can use a series of tests to determine diarrhea’s origin:

  • Fecal samples can reveal infectious causes, such as coronavirus, Salmonella, C. difficile and C. perfringens, and N. risticii, in addition to R. equi and rotavirus in foals.
  • Blood tests reveal hydration level, electrolyte balance, blood proteins, and pH.
  • Ultrasound can reveal thickened intestines, pinpoint specific segments of affected bowel, and identify abscesses, enlarged lymph nodes, or excess or infected fluids around the intestines.
  • Biopsy or abdominocentesis (sampling abdominal fluid using a hollow needle for testing) might reveal abnormal cells or bacteria.

If the cause of your horse’s diarrhea is infectious, Heidmann recommends isolating him and observing biosecurity measures for two full weeks following infection resolution.

Because both coronavirus and Salmonella are shed in feces, use dedicated stall-cleaning tools and dispose of manure without spreading it on fields, says Nolen-Walston. And be sure caretakers wear boots, gloves, and either change clothes or wear coveralls when mucking stalls.

Treatment Plans

Nolen-Walston’s go-to diarrhea treatment comprises three steps:

  1. Identify the causal agent and treat for it. In addition to diagnosis-specific treatments, most diarrhea cases need supportive care.
  2. Maintain adequate hydration.
  3. Treat endotoxemia. When they die, Gram-negative bacillus (rod-shaped) bacteria’s cell walls become highly toxic to horses.

“In a healthy horse’s gut, there’s normally enough endotoxin to kill 100 horses, but the gut has really tight junctions, so bacteria don’t leak out,” Nolen-Walston says. “But with diarrhea, the intestine becomes inflamed, and junctions can leak endotoxin into the bloodstream.

“Horses with endotoxemia have gums that are brighter pink to dark red or purple, sometimes with a purple line—called a toxic line—around their teeth,” she continues. “These horses have extremely low white blood cell counts. They’re treated with flunixin and other anti-endotoxic medications to reduce the inflammation that drives endotoxemia’s organ damage.”

Endotoxin causes fever, high heart rate, and uncontrolled inflammation across multiple organ systems throughout the horse’s body. “These horses can develop low blood pressure, hemorrhages, liver dysfunction, kidney necrosis (tissue death), and shock,” she says. “And although endotoxins themselves don’t cause laminitis, horses that have severe diarrhea and endotoxemia often develop organ failure that starts in the feet. Laminitis is probably the most common reason an equine colitis case doesn’t survive.”

Another way to treat endotoxemia is to give endotoxin-binding medication (polymyxin B). “We can also give plasma from horses that have been vaccinated against endotoxin so their antibodies will bind and disable it,” says Nolen-Walston. “We sometimes give clenbuterol, which is usually given to horses with asthma but also has anti-endotoxic effects.”

Charcoal or bentonite clay in powdered form (smectite clay; di-tri-octahedral smectite, known as Bio-Sponge) given via stomach tube can also absorb toxins. “It binds the toxins, and also binds the water so the horse loses fewer fluids in its diarrhea,” Heidmann says.

Restoring Normal Gut Flora


“There are some bacteria known to be associated with gut health,” Heidmann says, citing the yeast Saccharomyces boulardii, in particular, as being shown to help reduce the severity and duration of GI tract disease.

Other studies show lactic-acid-­producing bacteria might help reduce or prevent the growth of some pathogens and produce vitamins, enzymes, and volatile fatty acids that might promote GI health.

Nolen-Walston, however, sees two intrinsic problems with using probiotics to restore normal gut flora. First, she says, for a probiotic to be effective, you must know what flora are missing in the intestine and somehow be able to deliver them to the colon alive.

Second, many products test as having very low levels of the probiotics listed on the packaging. “Although it’s a lovely idea to be able to give back the missing ‘good’ bacteria, there’s very little evidence that a lot of the commercial products are that useful,” she says. “There are a few small studies that suggest possible efficacy of certain beneficial bacteria, but there’s not enough good information to be able to recommend them.”


Distasteful as it might sound, fecal transfaunation has proven effective for some diarrhea cases, including C. difficile. “It’s taking a healthy horse’s manure, filtering it, and then administering the material to a sick horse,” Heidmann says. “You’ll often see foals eating their mothers’ manure. It’s an instinctual habit to get the good bugs into their stomach. We only do that in the sickest cases, but in some instances it can be associated with resolution of clinical signs.”

Take-Away Message

Although not an all-inclusive list, now that you know the most common signs, causes, and treatments for diarrhea, you can more accurately judge the urgency of your horse’s case. But always err on the side of caution. “One of the biggest mistakes inexperienced horse owners make is not taking diarrhea seriously enough,” Nolen-Walston says. “It’s much more likely to be fatal in horses than in humans.”