A cough is a complex neurogenic reflex that forms part of the innate protective mechanisms of the airways. The function of coughing is to clear the airways of noxious stimuli (microbes, chemicals, and physical); however, many medical conditions, including those of the upper airways, evoke cough, which in itself may be a major symptom of the particular disease state. This chapter is structured to overview the neural and molecular mechanisms involved in the detection and reaction to stimuli, causes of cough with a focus on upper airway etiologies, and two case studies to contextualize this information.