Cilia and flagella are both hair-like structures that extend from cell surfaces and use coordinated movement to propel cells or move fluid around them. Both are composed of a core of microtubules surrounded by a cell membrane, featuring the same fundamental internal architecture called the axoneme—typically nine pairs of microtubules arranged in a circle with two central microtubules (the 9+2 arrangement). Both structures use dynein proteins that interact with microtubules to generate bending movements powered by ATP.
The key differences lie in size, number, and movement patterns. Flagella are longer and fewer in number—most organisms have one or a few flagella per cell—and they move with a whip-like, wave-like motion from base to tip that propels the entire cell forward. Cilia are shorter and more numerous, often covering a cell in hundreds, and they move with a more synchronized oar-like or rowing pattern, beating back and forth in coordinated waves. Structurally, cilia typically display a more synchronized metachronal rhythm (coordinated wave motion), while flagella generate helical or undulating waves.
Functionally, flagella are commonly found on sperm cells and many single-celled organisms like bacteria and protists, serving as primary propulsion. Cilia are found throughout animal bodies, including on cells lining the respiratory tract, fallopian tubes, and the trachea, where they move mucus and fluid rather than the cell itself. Some organisms like certain protozoans have both structures, and cells can have hundreds of cilia but rarely more than one or two flagella, reflecting their different roles in cellular transport and movement.