Cilia and flagella are microtubule-based, rod-shaped organelles present on the surface of a variety of eukaryotic cells. They function in cell locomotion, flow of extracellular fluid across cell surfaces as well as in detection, transmission and integration of signals from the cellular surroundings. In vertebrates, cilia are critical for regulating developmental processes and tissue homeostasis. Consequently, genetic defects that impair ciliary function or assembly lead to a growing number of different human diseases. This class of diseases, called ciliopathies, is often pleiotropic affecting multiple organs and tissues in the body. Here we first provide an overview of general cilia structure, and discuss mechanisms of ciliary assembly and length control, including intraflagellar transport (IFT) and transcriptional control of motile cilia formation. Next, we describe how cilia coordinate their motility and signaling functions, and we conclude with a brief overview of ciliopathies and the main symptoms associated with these diseases