Cilia are highly conserved microtubule-based organelles that arise from the cell surface and are required for cell motility, sensory and developmental functions. Defects in cilia cause a large number of diseases collectively known as ciliopathies. During ciliary assembly, tubulin subunits are transported between the base and tip of cilia through intraflagellar transport. The distal end of cilia is the site of addition and removal of tubulin subunits from the ends of microtubules. The tip is also the area where the switching of IFT motors (from kinesin-2 to cytoplasmic dynein) and the change of directionality of the IFT particle movement occur. Ultrastructural studies revealed that ciliary tips contain elaborate cap structures that plug the ends of microtubules and attach microtubules to the plasma membrane. Not much is known about the protein composition of the ciliary tips and not a single protein that is a component of the caps is known. The aim of this thesis was to identify a marker of the ciliary tip, which can then be used to determine the composition of the ciliary caps. Two approaches, candidate and proteomic, were used to obtain candidate marker proteins using the ciliated protist Tetrahymena thermophila as a model. Using a candidate approach, we evaluated kinesin-13, confirmedits transient association with the ciliary tip and unraveled its novel function in ciliary assembly and motility. Using a proteomic approach, we first pursued a conserved ciliary protein FAP206 but found that it only localizes to the tip of cilia when present in excessive quantity. Furthermore, we found that FAP206 is a repeated element of the middle axoneme segment, functioning as a microtubule-docking adapter for ciliary radial spoke 2 and dynein c. Finally, using the proteomic approach, FAP256, a centrosomal protein was found to localize at the distal tips of cilia when expressed at the native level.