Although the terms cilium and flagellum refer to similar structures, the structures were named when their internal similarities were not appreciated.
Cilia are short, numerous, and usually complexly organized.
Flagella are longer, fewer, and less complexly organized. In both cases, these nonmembranous organelles are minute, tubular extensions of the plasma membrane that surround a complex arrangement of microtubules. Cilia and flagella function to move whole cells or to move materials across or into cells. The underlying structure consists of nine microtubule doublets arranged in a cylinder around a central pair of microtubules. Various types of whipping movements of a whole flagellum or cilium occur when the microtubule doublets move relative to neighboring doublets.