Coughing can originate from either the upper respiratory tract or the lower respiratory tract. The upper respiratory tract refers to the nasal passage ways, larynx (throat) or the trachea. The lower respiratory tract refers to the lung itself. Coughing comes about from irritation of the lining of the airways or the lung itself having inflammation or increased fluid accumulation in the airways or the lung. Most, but not all, upper respiratory issues relate to some type of infectious process, such as viral or bacterial infections. These can involve inflammation or infection of the tissues lining the upper respiratory tract or structures of the airways such as the guttural pouches or sinuses that can retain fluid. The contagious causes of a cough are the infectious viral and bacterial agents such as influenza, rhinopneumonitis, rhinitis, equine viral arteritis and streptococcus equi. These infectious agents can cause issues in the lower respiratory tract from the primary infection. Problems also arise after the infection has resolved, yet the inflammation induced in the lung has not been eliminated. The non-infectious primary causes of a cough include lung worm, exercise induced pulmonary hemorrhage, inflammatory airway disease, and recurrent airway obstructive disease. Other causes such as neoplasia, summer pasture - associated obstructive pulmonary disease will not be discussed here.
Below is a diagram of the respiratory tract of the horse. For our purposes we will define the upper respiratory tract as beginning at the nostril and extending to where the trachea (windpipe) divides prior to entering the lungs; the lower tract is from this division all the way into the lungs. The analogy used to understand the lower respiratory tract would be a large oak tree. The oak tree has a trunk which rises from the ground before it divides into large branches, which extend further up and divide into smaller branches which extend further up, dividing into smaller branches before ultimately ending in the leaves. The trunk would equal the trachea, which divides into the major bronchi, which divide further into smaller bronchi which ultimate split into bronchioles which ultimately end in the alveoli (air sacs) - the alveoli being the leaves on the tree in our analogy. The alveoli are the site where the oxygen and carbon dioxide exchange take place.