Cilia and flagella of eukaryotic cells are evolutionarily conserved organelles with a microtubule-based axoneme as a scaffold. To fulfil their functions in cellular motility, sensory reception and developmental signalling, cilia contain unique proteins, such as receptors and ion channels. The assembly and maintenance of cilia depend on protein trafficking mediated by intraflagellar transport (IFT) particles as well as on selective entry and exit of proteins across the transition zone, which is located at the ciliary base. Bidirectional movement of IFT particles, which are composed of IFT-A and IFT-B complexes, is powered by kinesin-2 and dynein-2 motors. The BBSome associates with IFT particles and probably mediates the ciliary trafficking of membrane proteins. Abnormal ciliary assembly and functions due to defects in IFT particle components lead to a wide spectrum of disorders, which are collectively called the ciliopathies. We here review the IFT machinery by associating the architecture of the IFT complexes and their motor and cargo proteins with their functions.