Diarrhea in newborn foals can develop as a result of inflammation in the GI tract, decreased motility, increased secretion of fluid in the tract, and other causes. Studies show there are several risk factors for diarrhea in newborn foals, and one of these is using shavings as stall bedding as well as using antibiotics in the foals. You can decrease the incidence of foal diarrhea by disinfecting your foaling stalls, washing the mare's udder and tail before foaling, and foaling on pasture instead of in a stall.

Diarrhea can be due to an infection or may be non-infectious and the most common type of non-infectious diarrhea is foal heat diarrhea. Dr. Gary Magdesian indicates in the Clinician that foal heat diarrhea usually occurs from five to 21 days of age and usually resolves without any treatment. However, it is possible some of these foals can dehydrate and will require fluid therapy. It was previously thought that foals developed foal heat diarrhea when the mare came into heat and that a hormonal change in the mare's milk led to a foal's diarrhea. It was also believed by some that a parasite was the cause and to prevent this mares were dewormed immediately after foaling.

However, it is now known that the diarrhea is not due to changes in the mare's milk or a parasite but to normal maturation of the foal's GI tract. The bacteria in the foal's GI tract changes and becomes similar to the adult's normal flora by four weeks of age and the diarrhea usually resolves. So foal heat diarrhea is a normal sign that occurs in almost all foals and is due to the foal's initial ingestion of feed, plus ingesting the dam's feces if the tail is not washed prior to birthing.