The presence of cilia on epithelia of the respiratory tract was reported more than 150 yr ago, and the two-layer model of mucus transport was put forward more than 50 yr ago. However, it is only in the last 10 yr or so that the motion of mucus-propelling cilia of the mammalian respiratory system has been adequately described, and fluid dynamic studies have developed far enough to allow descriptions of the mechanisms by which ciliary movement is coupled to mucus transport. In this review, scientific developments on the study of cilia and mucus, and interactions between them, are drawn together to further understanding of mucociliary clearance mechanisms of the respiratory tract. The study of the cilia incorporates a discussion of the internal mechanics and biochemistry of the ciliary axoneme, the physical principles of the beat pattern, and the (weak) metachronal coordination of cilia in the lung. Mucus rheology plays a central role in mucociliary transport with the rheologic properties of the mucus determining the effective functioning of this clearance mechanism. Theoretical models provide information on the mechanical principles of the beat pattern as well as providing reliable estimates of the transport rates. Although airflow is not thought to contribute to mucus transport in the normal state, high frequency ventilation and coughing may make significant contributions.