According to Horse Owner's Veterinary Handbook, horses should never be given antibiotics unless they are sick, injured or undergoing surgery. This is because of the risk of side effects from antibiotics in horses.
Carrie Grustaven from the University of Illinois College of Veterinary Medicine points out that horses can have sores, swelling and abscesses at the area where the antibiotic was injected.
According to Current Therapy In Equine Medicine, diarrhea is a common and potentially dangerous side effect of antibiotics because it causes dehydration.
Other effects include colitis, causing a secondary infection and an allergic reaction, usually with hives and problems breathing. This allergy can kill the horse.
Long-term effects of antibiotics in horses include damage to the liver and kidneys as well as antibiotic resistance. This is when the bacteria causing the illness have adapted to combat the antibiotic in the body of the horse.
The antibiotics tetracycline and griseofulvin should never be given to pregnant mares, according to Horse Owner's Veterinary Handbook, because they can cause birth defects in foals.