The ventricular system in the brain is lined by multiciliated cells. The motility of these ependymal cilia was analyzed in hy3-/- mice which carry a null mutation in Hydin and develop lethal hydrocephalus. Hy3-/- cilia lack a projection from the ciliary central pair and move with slightly reduced beat frequency and a greatly reduced beat amplitude. They lack the ability to generate fluid flow explaining the hydrocephalic phenotype of the mutant mice. The assembly of motile and non-motile cilia requires intraflagellar transport (IFT) but it remains largely unknown how IFT traffics ciliary precursors. Simultaneous in vivo imaging of IFT and cargoes revealed a complex pattern of IFT and non-IFT cargo movements, and unloading and assembly site docking events. Quantitative data on cargo frequency, assembly, and turn-over will provide a basis for future modeling of ciliary assembly and dynamics.