Researchers have reported that between 50% and 80% of all foals develop at least one bout of diarrhea in the first six months of their lives. Severity can vary from a mild, self-limiting case, such as what breeders frequently see during foal heat diarrhea, to profuse watery diarrhea that results in dehydration, depression, weakness, recumbency, and potentially death.

“Given that foals with diarrhea can decline rapidly, immediate veterinary examination, intervention, and management are required,” says Michael Mienaltowski, DVM, PhD, associate professor in the University of California, Davis, College of Veterinary Medicine.

Causes of Diarrhea in Foals

In addition to the largely benign foal heat diarrhea occurring between five and 15 days of life, dietary imbalances, intestinal lining irritation secondary to pica (a propensity for consuming nonfood items), and lactose intolerance can also cause noninfectious diarrhea.

An estimated 20% of diarrhea cases in foals are believed to be associated with infectious agents (Basso et al., 2026), including equine coronavirus, Clostridioides difficile, Clostridium perfringens, Lawsonia intracellularis, Cryptosporidium spp, Salmonella spp, Rhodococcus equi, and even internal parasites. By far the most common cause of infectious diarrhea in foals, however, is rotavirus.

Rotavirus A (RVA) primarily occurs in young foals (less than 3 months old) and causes an estimated 21% of cases. “Foals from unvaccinated dams typically get sick at a very young age (between birth and 1 week old) whereas foals from vaccinated dams typically develop diarrhea when they are a couple months old,” says Lianne Eertink, PhD, research scientist II at the University of Kentucky’s Maxwell H. Gluck Equine Research Center, in Lexington. “This is thought to be due to the decrease in maternal antibodies in foals over time. In general, the older the foal is, the less severe the disease is.”

“Rotavirus A typically causes disease outbreaks due to the fact it is highly contagious, replicates quickly, and is shed in high concentrations in foals’ feces,” says Feng Li, DVM, PhD, the William Robert Mills Chair in Equine Infectious Disease, also at the Gluck Center. “The incubation period is rapid, between one and four days, but foals can begin shedding RVA prior to developing diarrhea and can continue to shed for 12 days following resolution of the diarrhea.”

RVA causes diarrhea using two distinct mechanisms. First, it injures the nutrient-absorbing region of cells of the small intestine, causing a malabsorptive diarrhea. Second, it produces nonstructural glycoprotein 4 (NSP4), a toxin responsible for the hypersecretory (excess water and electrolyte secretion) component of the disease.

“It is important to note that RVA typically only harms the tips of the villi, where most of the lactase-producing cells are,” adds Li. “Subsequently, foals become lactose intolerant, and it is therefore recommended to not let foals nurse.”

Gut Microbiome Disruption to Foal Diarrhea

“The intestinal microbiome includes communities of beneficial microbes living in a horse’s gut that help break down hay, grass, and other feeds that a horse cannot fully digest on its own,” says Mienaltowski. “These microbes produce nutrients and energy; they also promote gut health and immunity. When dysbiosis (gut microbial imbalance) occurs, such as with colitis, the balance of the beneficial microbes is disrupted, and other microbes, including pathogenic bacteria, can grow and flourish. This reduces digestion efficiency, impacts intestinal water balance, can lead to inflammation, diarrhea, and rapidly to dehydration in a foal.”

To better understand the intestinal microbiome changes that occur in foals with diarrhea, Mienaltowski and colleagues collected fecal samples from 19 foals aged 3 to 143 days with watery diarrhea. They performed standard laboratory analyses on those samples to identify any pathogens as well as the bacterial populations in those samples making up the intestinal microbiome.

Ten samples were negative for pathogens, and the remaining nine samples tested positive for C. perfringens and/or C. difficile toxins.

“Foals with pathogen-associated diarrhea had significantly lower gut microbial diversity and distinct microbial populations compared to foals with nonpathogenic diarrhea, Mienaltowski says.

Treating Foal Diarrhea

Veterinarians typically manage foals with diarrhea symptomatically using intravenous fluids, toxin-binding agents, and nutritional support. Depending on the underlying causes, they might also administer antibiotics.

In addition, practitioners are turning to fecal microbial transplantation (FMT) more often to treat diarrhea. This procedure, designed to restore the sick foal’s microbiota, involves administering a slurry of feces from a disease-free donor horse via nasogastric (NG) intubation. In a recent study survival and duration of diarrhea was not different between foals receiving FMT and foals treated with an electrolyte solution (also via NG tube); however, other clinical and clinicopathologic findings were improved, and researchers deemed the FMT procedure safe. As a result, they suggest a beneficial effect of FMT on the gastrointestinal microbiota could not be discounted and recommend additional research (Bell et al., 2024).

Rotavirus Vaccines for Horses

Addressing the importance of RVA, a killed vaccine was released in 1996 to vaccinate mares at eight, nine, and 10 months of gestation. The resultant antibodies in the mare against RVA then pass onto the foals through colostrum, the foal’s first milk.

“This maternal vaccine has substantially reduced RVA outbreaks and mitigated (the pathogen’s) effect on foal health,” says Li. “However, maternal antibodies decline steadily after birth, reaching very low levels by two to four months of age. Vaccinating the foals directly may improve immunity to RVA.”

Veterinarians generally believe foals should not be vaccinated before 6 months old because their immune systems have not developed fully and they cannot respond to vaccination well, says Eertink. “However, there a few pathogens they do respond to well to vaccination, and rotavirus seems to be one of these,” she adds.

Eertink, Li, and colleagues therefore elected to use the vaccine off label in the foals instead of the mares. Li says researchers on previous studies showed vaccinating foals against RVA at 1 month old wasn’t effective. But in Li’s pilot study, foals vaccinated at 2 and 3 months old mounted an immune response while maintaining protective antibody levels. Unlike maternal antibodies, which naturally decline over time, that response helps generate longer-lasting immunity.

Also seeking to create an RVA vaccine, a research team led by Noah Cohen, VMD, MPH, PhD, Dipl. ACVIM-LA, professor of equine medicine at Texas A&M’s College of Veterinary Medicine & Biomedical Sciences, in College Station, vaccinated pregnant mares with a novel VP8* vaccine or the commercially available killed RVA vaccine.

“We found longer-lasting, higher concentrations of virus-neutralizing antibodies with the VP8*mRNA vaccine than the killed RVA vaccine,” says Cohen. “This suggests the VP8* vaccine would provide superior duration of immunity to RVA in foals born to mares vaccinated with the VP8* mRNA.”

Additionally, Cohen said they are conducting a follow-up study using a “VP8* mRNA vaccine modified to provide stronger and longer immunity in foals.”

Take-Home Message

Timely diagnosis and appropriate treatment of diarrheic foals results in improved survival rates, but the cost of disease can be high. Focusing on preventive strategies, such as vaccination, might help mitigate those costs and improve foal welfare.