Cilia are complex and powerful cellular structures that serve a multitude of functions across many types of organisms. In humans, one of the most critical roles of cilia is defense of the airway. The respiratory epithelium is lined with cilia that normally carry out an integrated and coordinated mechanism called mucociliary clearance. Mucociliary clearance, the process by which cilia transport the viscous mucus blanket of the upper airway to the gastrointestinal tract, is the primary means by which the upper airway clears itself of pathogens, allergens, debris, and toxins. The complex structure and regulatory mechanisms that dictate the form and function of normal cilia are not entirely understood, but it is clear that ciliary dysfunction results in impaired respiratory defense. Ciliary dysfunction may be primary, the result of genetic mutations resulting in abnormal cilia structure, or secondary, the result of environmental, infectious or inflammatory stimuli that disrupt normal motility or coordination.