Cilia are hair-like structures that can beat in synchrony causing the movement of unicellular paramecium. Cilia are also found in specialize linings in eukaryotes. For example, cilia sweep fluids past stationary cells in the lining of trachea and tubes of female oviduct.

Flagella are whip-like appendages that undulate to move cells. They are longer than cilia, but have similar internal structures made of microtubules. Prokaryotic and eukaryotic flagella differ greatly.