Cilia and flagella are made up of microtubules, which are composed of linear polymers of globular proteins called tubulin. The core (axoneme) contains two central fibers that are surrounded by an outer ring of nine double fibers and covered by the cellular membrane.
These motile appendages are constructed by basal bodies (kinetostomes), which also function as centrioles. The basal body is located at the base of each filament, anchoring it to the cell and controlling its movement. Cilia and flagella have the same structure. The only difference is that the flagella are longer.
For single-celled eukaryotes, cilia and flagella are essential for the locomotion of individual organisms. Protozoans belonging to the phylum Ciliophora are covered with cilia. Flagella are a characteristic of the protozoan group Mastigophora.
In multicellular organisms, cilia function to move fluid or materials past an immobile cell as well as moving a cell or group of cells. The respiratory tract in humans is lined with cilia that keep inhaled dust, smog, and potentially harmful microorganisms from entering the lungs. Cilia generate water currents to carry food and oxygen past the gills of clams and transport food through the digestive systems of snails. Flagella are found primarily on gametes, but also create the water currents necessary for respiration and circulation in sponges and coelenterates.
Information provided by: http://micro.magnet.fsu.edu