Cilia and flagella are cell organelles that are structurally similar but are differentiated based on their function and/or length. Cilia are short and there are usually many (hundreds) cilia per cell. On the other hand, flagella are longer and there are fewer flagella per cell (usually one to eight). Though eukaryotic flagella and motile cilia are structurally identical, the beating pattern of the two organelles can be different. The motion of flagella is often undulating and wave-like, whereas the motile cilia often perform a more complicated 3D motion with a power and recovery stroke.

Comparison chart

Cilia versus Flagella comparison chart
Edit this comparison chartCiliaFlagella
Definition Cilia are short, hair like appendages extending from the surface of a living cell. Flagella are long, threadlike appendages on the surface of a living cell.
Cross section Nexin arm present. Nexin arm absent.
Length Short Longer than cilia, can vary
Motion Rotational, like a motor, very fast moving Wave-like, undulating, sinusoidal, slow movement compared to cilia
Density Many (hundreds) per cell Few (less than 10) per cell
Found in Eukaryotic cells Eukaryotic and prokaryotic cells
Etymology Pronounced as ‘silly-ah’, is the plural of cilium. From Latin word for eyelash. Pronounced as ‘fla-gel-ah’, is the plural of flagellum. From Latin word for whip.

Video Explaining the Difference

This video explains the difference between cilia and flagella, as well as the function and structure of these cell organelles.

Differences in structure

Difference between the movement of cilia and flagella
Difference between the movement of cilia and flagella

Eukaryotic motile cilium and flagellum are structurally identical. Each is a bundle of nine fused pairs of microtubule doublets surrounding two central single microtubules. The movement of both cilia and flagella is caused by the interactions of these microtubules.

In non-motile or primary cilia the two central single microtubules are absent. So the central bundle consists of 9 + 0 microtubules. In prokaryotes cells the flagella are filamentous protein structures composed of flagellin. Prokaryotic flagella are much thinner than eukaryotic flagella, and they lack the typical 9 + 2 arrangement of microtubules.

Types of cilia and flagella

There two types of cilia - motile and non-motile or primary cilia.

There are three types of flagella - bacterial, archaeal and eukaryotic.


Lack of proper functioning of cilia and flagella can cause several problems in human beings. For example,


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"Cilia and Flagella." Diffen LLC, n.d. Web. 9 Aug 2020. < >