Since the lungs are exposed to a fresh bombardment of dust particles, irritants and pathogens such as bacteria, fungi or viruses with every breath, an effective clearance system is essential. The smallest particulate pollutants are assimilated and decomposed in the alveoli, mainly by macrophages.

Outside the alveoli, the function of the mucociliary clearance system is assured by ciliated epithelia, which cover the entire respiratory tract. The surface of these epithelial cells is in turn covered with fine hairs, the cilia. The cilia are surrounded by a fluid mucous layer, the periciliary liquid. This ciliary layer is covered by the viscous mucus that traps foreign matter and microorganisms. The coordinated movement of the cilia in the periciliary liquid - like a cornfield in the wind - transports the mucus together with foreign matter towards the mouth, where it can be swallowed or coughed up.

The efficiency of this clearance mechanism depends on the number of cilia, their structure and motility, and the quantity and consistency of the mucus. If the muciliary clearance function is disrupted, as happens for example in cystic fibrosis or Kartagener syndrome, the effects can be severe, sometimes life-threatening.