Cough is most often do to aspiration of milk. Examination for hard palate deformities, neurological disease, and developing secondary pneumonia should be undertaken.

Age is important because their are diseases that effect foals that are not common in adults. Foals are susceptible to round worms who have as part of their life cycle migration through the foals lungs. Unless the deworming program has been very good round worms should be on the list of possibilities. Foals are also susceptible to a serious respiratory disease caused by a common soil contaminating organism, Rhodococcus. It causes a chronic abscessing pneumonia which may first present as a light cough and should always be considered in foals because without early diagnosis the foal will develop serious permanent damage to his lungs. Often foals with these type problems are on a farm with a history of such problems but should not be ruled out on this alone. The suspicion of Rhodococcus should be raised if the foal was born or been raised in a dusty environment as it greatly increases the exposure to the organism.

This group of horses most often have coughs without fever associated with recovering respiratory infection.

A common presentation is a deep cough that occurs when a horse is first exercised and disappears as the horse works and often referred to as a barn cough. Some horses will do this for years and years without worsening symptoms but it can be a harbinger of a serious developing condition: allergies to hay molds. With continued exposure to hay molds the allergy becomes worse until a allergic pneumonia develops that interferes with normal breathing and the horse is termed "heevy". Beside the cough, the breathing takes on a labored appearance. In spite of this the horse remains bright and alert with a good appetite at least until the breathing becomes so hard that it is hard to eat and breath at the same time. The source of the hay molds is the barn air and the hay itself.

A chronic cough after recovering from a respiratory infection is also a common event. Though usually not a difficult diagnosis because of the past history of a snotty nose and fever occasionally the actual infection was mild enough to go unnoticed and the cough the only symptom. The cause can be either a mild bronchitis or irritation to the back of the throat a pharyngitis. Sometimes polyps can form in the back of the throat and cause a long lasting cough. Like the allergic horse this cough can worsen with exercise but does not tend to improve with more exercise and many even worsen the longer the horse is ridden.

Donkeys and mules can harbor infections of lungworms that can spread to horses. Lungworms settle in the lungs of horses but do not finish their life cycle so the horse is a dead end host for lungworms. Fecal float tests of the donkeys and mules might reveal the infection. Routine effective deworming is curative and should prevent this from happening.