The two most common reasons why horses cough are respiratory infection and recurrent airway obstruction (RAO), also known as heaves:

Respiratory infection

Horses are subject to viral respiratory infections including equine influenza and rhinopneumonitis. Along with a harsh, dry cough, a horse suffering from influenza may run a fever, have a runny nose, lose his appetite, be depressed, and exhibit muscle stiffness (similar to how you feel when you have the flu!) Rhinopneumonitis symptoms are similar.

It may not be clear which virus is affecting your horse without your veterinarian running laboratory tests, and unless your horse is a mare in foal (the rhinopneumonitis virus can cause abortion in pregnant mares), is extremely sick or develops complications, it probably doesn’t make much difference. Since both are contagious, however, a sick horse should be isolated from others in the barn until his symptoms have disappeared.

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