The lungs and the nasal passages are continually exposed to respiratory pathogens, toxins, and particulate matter, and have evolved a very effective defense system to protect themselves. Mucociliary clearance is an essential part of this defence and relies on appropriate interactions between the ciliated epithelium, the height of the periciliary fluid, and mucus. Mucus acts as a physical barrier, trapping inhaled particles and pathogens, whilst cilia move both the mucus layer and fluid in the underlying periciliary layer. These defenses may be disrupted by viral and bacterial infections, by inhaled toxins, and by inherited diseases such as primary ciliary dyskinesia and cystic fibrosis.