Cilia and flagella appeared very early in evolution to provide unicellular organisms with motility in water. Adaptation to non-aquatic life in plants resulted in the almost complete elimination of these organelles, except for gametic transport in some phylogenetic groups. In contrast, cilia and flagella were retained and employed for a wide variety of functions requiring fluid movement in complex multicellular animals. The functions of cilia in diverse processes such as left-right axis pattern formation, cerebrospinal fluid flow, sensory reception, mucociliary clearance and renal physiology indicate that cilia have been adapted as versatile tools for many biological processes. In this review, we discuss recent discoveries that have extended knowledge of the roles of cilia in normal development, and the pathological consequences caused by their dysfunction in mammals. We also consider evolutionary relationships between cilia from lower and higher eukaryotes, outline the ciliary components required for assembly and motility, and review the terminology of axonemal heavy chain dynein genes.