The cilium, plural cilia (from Latin 'eyelash'), is a membrane-bound organelle found on most types of eukaryotic cell, and certain microorganisms known as ciliates. Cilia are absent in bacteria and archaea. The cilium has the shape of a slender threadlike projection that extends from the surface of the much larger cell body. Eukaryotic flagella found on sperm cells and many protozoans have a similar structure to motile cilia that enables swimming through liquids; they are longer than cilia and have a different undulating motion.

There are two major classes of cilia: motile and non-motile cilia, each with a subtype, giving four types in all. A cell will typically have one primary cilium or many motile cilia. The structure of the cilium core called the axoneme determines the cilium class. Most motile cilia have a central pair of single microtubules surrounded by nine pairs of double microtubules called a 9+2 axoneme. Most non-motile cilia have a 9+0 axoneme that lacks the central pair of microtubules. Also lacking are the associated components that enable motility including the outer and inner dynein arms, and radial spokes. Some motile cilia lack the central pair, and some non-motile cilia have the central pair, hence the four types.

Most non-motile cilia are termed primary cilia or sensory cilia and serve solely as sensory organelles. Most vertebrate cell types possess a single non-motile primary cilium, which functions as a cellular antenna. Olfactory neurons possess a great many non-motile cilia. Non-motile cilia that have a central pair of microtubules are the kinocilia present on hair cells.

Motile cilia are found in large numbers on respiratory epithelial cells – around 200 cilia per cell, where they function in mucociliary clearance, and also have mechanosensory and chemosensory functions. Motile cilia on ependymal cells move the cerebrospinal fluid through the ventricular system of the brain. Motile cilia are also present in the fallopian tubes of female mammals where they function in moving the egg cell from the ovary to the uterus. Motile cilia that lack the central pair of microtubules are the cells of the embryonic primitive node termed nodal cells and these nodal cilia are responsible for the left-right asymmetry in bilateral animals.