Cilia and Flagella

Ciliated Epithelial Cells
This colored scanning electron micrograph (SEM) of a section through the wall of a trachea (wind pipe) shows ciliated epithelial cells. Steve Gschmeissner/Science Photo Library/Getty Images

What Are Cilia and Flagella?

Both prokaryotic and eukaryotic cells contain structures known as cilia and flagella. These extensions from the cell surface aid in cell movement. They also help to move substances around cells and direct the flow of substances along tracts. Cilia and flagella are formed from specialized groupings of microtubules called basal bodies. If the protrusions are short and numerous they are termed cilia. If they are longer and less numerous (usually only one or two) they are termed flagella.

What Are Their Distinguishing Characteristics?

Cilia and flagella have a core composed of microtubules that are connected to the plasma membrane and arranged in what is known as a 9 + 2 pattern. The pattern is so named because it consists of a ring of nine microtubule paired sets (doublets) that encircle two singular microtubules. This microtubule bundle in a 9 + 2 arrangement is called an axoneme. The base of cilia and flagella is connected to the cell by modified centriole structures called basal bodies. Movement is produced when the nine paired microtubule sets of the axoneme slide against one another causing cilia and flagella to bend. The motor protein dynein is responsible for generating the force required for movement. This type of organization is found in most eukaryotic cilia and flagella.

What Is Their Function?

The primary function of cilia and flagella is movement. They are the means by which many microscopic unicellular and multicellular organisms move from place to place. Many of these organisms are found in aqueous environments, where they are propelled along by the beating of cilia or the whip-like action of flagella. Protists and bacteria, for example, use these structures to move toward a stimulus (food, light), away from a stimulus (toxin), or to maintain their position in a general location. In higher organisms, cilia is often used to propel substances in a desired direction. Some cilia, however, do not function in movement but in sensing. Primary cilia, found in some organs and vessels, can sense changes in environmental conditions. Cells lining the walls of blood vessels exemplify this function. The primary cilia in blood vessel endothelial cells monitor the force of blood flow through the vessels.

Where Can Cilia and Flagella Be Found?

Both cilia and flagella are found in numerous types of cells. For instance, the sperm of many animals, algae, and even ferns have flagella. Prokaryotic organisms may also possess a single flagellum or more. A bacterium, for example, may have: one flagellum located at one end of the cell (montrichous), one or more flagella located at both ends of the cell (amphitrichous), several flagella at one end of the cell (lophotrichous), or flagella distributed all around the cell (peritrichous). Cilia can be found in areas such as the respiratory tract and female reproductive tract. In the respiratory tract, cilia helps to sweep mucus containing dust, germs, pollen, and other debris away from the lungs. In the female reproductive tract, cilia helps to sweep sperm in the direction of the uterus.

More Cell Structures

Cilia and flagella are two of the many types of internal and external cell structures. Other cell structures and organelles include:

  • Cell Membrane: This outer membrane of eukaryotic cells protects the integrity of the interior of the cell.
  • Cytoskeleton: The cytoskeleton is a network of fibers that forms the internal infrastructure of the cell.
  • Nucleus: Cell growth and reproduction are controlled by the nucleus.
  • Ribosomes: Ribosomes are RNA and protein complexes that are responsible for protein production via translation.
  • Mitochondria: These organelles provide energy for the cell.
  • Endoplasmic Reticulum: Formed by the infolding of the plasma membrane, the endoplasmic reticulum synthesizes carbohydrates and lipids.
  • Golgi Complex: This organelle manufactures, stores, and ships certain cellular products.
  • Lysosomes: Lysosomes are sacs of enzymes that digest cellular macromolecules.
  • Peroxisomes: These organelles help to detoxify alcohol, form bile acid, and use oxygen to break down fats.


  • Boselli, Francesco, et al. “A quantitative approach to study endothelial cilia bending stiffness during blood flow mechanodetection in vivo.” Methods in Cell Biology, Vol. 127, Elsevier Academic Press, 7 Mar. 2015,
  • Lodish, H, et al. “Cilia and Flagella: Structure and Movement.” Molecular Cell Biology, 4th ed., W. H. Freeman, 2000,
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Bailey, Regina. "Cilia and Flagella." ThoughtCo, Aug. 27, 2020, Bailey, Regina. (2020, August 27). Cilia and Flagella. Retrieved from Bailey, Regina. "Cilia and Flagella." ThoughtCo. (accessed March 20, 2023).