Despite their large, powerful stature, horses have relatively small, simple stomachs, and any type of unnatural horse-keeping can lead to gastrointestinal (GI) problems. As grazing animals, horses are designed to have small amounts of food continually moving through their digestive tracts with fibrous feeds that are mainly fermented in the hindgut (cecum and colon). Unfortunately, modern-day horse-keeping makes it challenging for most sporthorses to access pasture 24/7. Providing your horse with hay in his stall can help supplement his forage needs, but depending on his schedule, this might still result in sporadic meals.

In this article, Frank Andrews, DVM, M.S., Dipl. ACVIM and director of equine health and sports performance at Louisiana State University, and Anthony Bliksager, DVM, Ph.D. and director of veterinary medical services at North Carolina State University College of Veterinary Medicine, explain the different issues that can arise along a horse’s GI tract. Blikslager is an equine surgeon who sees many GI tract problems. “These are still prevalent in spite of the many ways we try to prevent and treat them,” he says.

Squamous and Glandular Ulcers in the Stomach

Gastric (stomach) ulcers often occur in the squamous epithelium, the tissue in the top portion of the stomach, and are referred to as squamous, or nonglandular, ulcers. They are thought to be less problematic because they heal more quickly and are less painful than ulcers in the lower part of the stomach. “An athletic horse is more active than a horse at pasture. When a horse exercises, stomach acid tends to slosh into the upper part. It’s like reflux esophagitis—or heartburn—in people,” says Blikslager. Unlike a human’s stomach that only produces acid when eating, acid production is continuous in a horse’s stomach. In natural conditions when there is always forage in the stomach, the acid helps digest it.

Andrews says each part of the GI tract has a different pH. “The pH scale is 0 to 14, with 7 being neutral. Acids have a pH less than 7, while bases (alkaline substances) have a pH greater than 7,” he says.

Horses’ stomach contents must be very acidic for digestion, with the pH being between 1 and 3. “As partially-digested food goes into the duodenum—the first part of the small intestine—the pH goes up to about 8, so it is alkaline. This helps with absorption of nutrients,” Andrews explains.

“Gastric ulcers commonly occur in horses involved in intense exercise. We see the most ulcers in racehorses, but also many in warmbloods,” Andrews says. Risk factors include exercising more than five days a week, stress and a high-energy diet. Horses doing strenuous work are generally fed a lot of concentrate or grain, which can exacerbate the issue. 

While squamous ulcers in the upper stomach are common, ones in the lower stomach are being identified more with the advent of longer endoscopes exploring deeper into the stomach. “We now recognize ulcers in the lower, glandular, pink part of the stomach. These occur frequently in warmbloods and large sporthorses,” says Andrews. 

He noted a study that showed horses with glandular ulcers had high levels of cortisol, the hormone produced during periods of stress. For sporthorses, they may experience stress during trailering, stall confinement and when they have little or no access to pasture.

To check for glandular ulcers, the stomach must be completely empty, which takes about 24 hours. “You don’t want any feed down around the pylorus (the valve connecting the stomach and the duodenum),” Blikslager says. “There can be ulcers around that exit because injurious contents tend to concentrate there, like acid, bile and pepsin (a digestive enzyme). Even fermentation products from the food (short-chain fatty acids, such as butyrate or acetate) will be concentrated in that location.”

Treatment for Squamous and Glandular Ulcers

Gastric ulcers in horses can often be remedied with antacids along with management and diet changes. “The leading medication is still omeprazole, a proton pump inhibitor similar to over-the-counter products for people,” Blikslager says. “Equine products include enteric-coated omeprazole, long-acting omeprazole or injectable omeprazole. You can give one injection per week and not have to give the paste every day, but it is expensive.”

Because sporthorses require a lot of energy and are fed concentrates, which requires the stomach fluid to have a pH of 4 or below, horse owners should provide as much hay as possible to buffer the stomach acid. “Forage can form a mat on top of the acid contents and reduce sloshing into the upper part of the stomach,” Blikslager says. “You can also use a pelleted concentrate feed that contains forage.”

Glandular ulcers in the lower stomach aren’t as easy to heal with omeprazole alone. Another medication often added is misoprostol, a synthetic prostaglandin E1 (PGE1) analog. “It works by mimicking the body’s natural prostaglandins, which help regulate stomach acid. Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit prostaglandins,” Blikslager says. “Misoprostol can replace prostaglandin if you are using NSAIDs. Even by itself, misoprostol helps restore normal epithelial replenishment and blood supply to the GI tract.”

Additionally, try to reduce your horse’s stress by using different stabling and trailering practices, such as with a buddy or in an open stock trailer where he can move around. Since horses rarely stand still very long in natural conditions, Blikslager recommends walking your horse for 20 minutes several times a day while at a show. “When horses are stuck in a stall or trailer, we may not consider the important effect of exercise on GI tract motility and gut health,” he says.

Ulcers in the Small Intestine

Unfortunately, ulcers can extend beyond the stomach into the small intestine. “Anywhere in the GI tract can become ulcerated,” Blikslager says. “I occasionally see ulcers in the small intestine while performing surgeries.” 

An adult horse’s small intestine is approximately 70 feet long, and the primary site for digestion and absorption of nutrients. The small intestine has three segments. The duodenum is short—about 3 feet—where enzymes from the pancreas and liver begin to break down food. Bile is secreted from the liver to emulsify fats. The jejunum is 65 to 67 feet long, where most nutrients are absorbed. The ileum is the shortest—the last 1 to 2 feet—before it connects to the cecum. 

Blikslager explains that veterinarians suspected ulcers on the pylorus, but they couldn’t confirm them until longer endoscopes were available. “A horse might get a clean bill of health and still have ulcers if we don’t look clear through the stomach,” says Blikslager. Ulcers in the small intestine can be treated with omeprazole and misoprostol.

Problems in the Hindgut: Colon and Cecum

The horse’s hindgut is designed for fermenting forage, and the main nutrients derived here are short-chain (or volatile) fatty acids. “These are usually in manageable concentrations so horses can readily absorb them,” Blikslager explains. “But if there’s too much concentrate in the diet, feed can sometimes ferment too rapidly or abnormally, which creates problems.”

Anytime you make a change in your horse’s diet, do it gradually over several weeks. Without adaptation to increase sugar absorption, the sugar escapes absorption in the small intestine and enters the hindgut, which can change the colonic pH. The pH of the colon should be neutral (about 7), which allows good bacteria—mostly gram-negative—to ferment poorly-digestible hay and low-quality forage to produce short-chain fatty acids—acetic, butyric and propionic acids—which are absorbed to generate energy. Most of the energy that horses get from food comes from fermentation in the hindgut—not from glucose absorption in the small intestine. 

Too much grain or sugar in the hindgut negatively affects the horse’s microbiome. “A normal microbiome is complex and very individual from one horse to another, but some shifts in the microbiome are not helpful,” Blikslager says.

“If grain makes it into the hindgut, it’s also fermented. This creates an overgrowth of ‘bad’ bacteria (gram-positive bacteria) that produce lactic acid, leading to a drop in colonic pH (colonic acidosis). When the pH drops, there is more gas production and inflammation of the lining of the colon, which might produce more gas, flatulent colic or even laminitis,” Andrews says.

Blikslager explains that continuous fluctuations in the microbiome or a diet that isn’t optimal and creates more acid-based content can erode the lining of the hindgut, similar to what’s seen in the stomach. Ulceration occurs most frequently in the right dorsal colon. “This area doesn’t have as many protective factors; the problem may be related to poor blood supply, bicarbonate transport or buffering capacity,” he says. “Everything is concentrated there, like in the pylorus of the stomach; the contents are ready to go to the final part of digestion, into the small colon.”

The right dorsal colon is often affected by NSAIDs, which Blikslager says may be due to inherent sensitivity to those drugs or—more likely—because of an imbalance of the protective factors (including prostaglandins). “If you diminish prostaglandins in an area that’s already borderline, this can create problems,” he says.

Not all NSAIDs carry the same risk of affecting the hindgut. Phenylbutazone (bute), a potent NSAID, is most commonly associated with causing hindgut issues. Blikslager says it can shut down the whole prostaglandin cascade. Other NSAIDs that affect the colon include flunixin meglumine (Banamine^®), ketoprofen (Ketofen^® or KetoMed™) and firocoxib (Equioxx^®). Blikslager says that while firocoxib is a more selective NSAID, targeting cyclooxygenase-2 (COX-2) that over-produces prostaglandins involved in inflammation, COX-2 has a dual role.

“It is helpful in the gut because mucosal repair is stimulated by prostaglandins, particularly PGE2, which is similar to misoprostol, PGE1. In the gut, prostaglandins are generally protective,” he says. “Many horses today are on one tablet of Equioxx daily, which usually works well, but it may add trouble if you have a horse that has a problem with his colon.”

Diagnosing issues in the hindgut can be challenging. Veterinarians are unable to explore the colon with an endoscope, but they can palpate or ultrasound the area. However, this has its limitations. “We can ultrasound to see how thick the colon is—thickening is associated with inflammation. But we are generally just looking at the surface with ultrasound, and when palpating, we are only reaching about one-third,” Blikslager says. “It is a difficult organ to figure out what’s going on.”

Prevention of hindgut issues includes reducing stress and making sure the horse is well hydrated. Owners should gradually acclimate their horses when transitioning from grazing on pasture to being fed dry hay and shipping to a show. “Going from 90% water feed (green grass) to 90% dry matter feed, horses become dehydrated,” Andrews says. “When dry hay hits the colon, water is sucked from the bloodstream to try to moisten and digest the hay.”

Is It a Gastric or Hindgut Problem?

Signs of gastric and hindgut problems often overlap and can include anything from colic to behavioral changes. “If the colon is going back and forth with excess fluid and decreased fluid—and maybe mild impactions—you might see colic,” Blikslager says.

He adds that trainers and owners generally think about gastric ulcers in terms of behavioral changes, but colonic ulcers might also have subtle effects on performance and behavior as well as more obvious signs like colic. Individual horses react differently to pain, and horses can have gastric and hindgut issues at the same time.  

Horse owners can watch for changes in manure consistency as a possible indication of a hindgut problem due to the colon trying to compensate with fluid. “The horse’s body has mechanisms to pour fluid into the colon, and retrieve it, but problems that arise from changes in the microbiome and digestion can cause intermittent loose stool,” Blikslager says. “Some horses have that problem anyway, but if it’s associated with clinical signs, it could indicate a hindgut problem.”

It’s hard to say how some of these issues affect sporthorses. It depends on the individual. “Some are very stoic and keep performing, but any small adjustment you can make to help the horse might make a difference,” Blikslager says. “It might only add a percentage point to your dressage score, but that could make a big difference in your horse’s well-being.”

Research on the Equine GI Tract

Current equine GI research is focusing on proton pump inhibitors as well as defining the parameters of a normal microbiome. Blikslager notes that Purina is researching the horse’s microbiome, and some labs across the country are collecting samples of normal fecal material. “The biome is incredibly different horse to horse, but researchers are trying to figure out how different it can be before it’s considered abnormal,” he says. “We need a massive data set to figure out where these different species of ‘gut bugs’ should be, numerically. Then, we could determine what is outside that range.”

Another area of research focuses on probiotics. Blikslager notes that it is unclear how much to give, how much of the products reach the colon, whether they contain the right organisms and whether the organisms are live by the time they reach the colon. However, he adds that lactobacillus seems to be the most helpful organism in probiotics. 

While Blikslager doesn’t see any harm in feeding probiotics, he says the true benefits are unclear. “Some companies are trying novel approaches to protect the product from stomach acid and increasing the number of organisms in the product, but what comes through on the other end is not well understood,” he says.

For More:

• Read more about the architecture of the equine digestive system, here. 
• Learn why quality forage is essential for your horse’s health and performance here.

This article originally appeared in the winter 2025 issue of Practical Horseman.