cross-section of two motile cilia, showing the "9+2" structure

A cilium (plural cilia) is a fine projection from a eukaryotic cell. There are two types of cilia: (1) motile cilium, which constantly beats in one direction, and (2) non-motile cilium, which cannot beat and usually serves as a sensor.

Cilia are structurally identical to eukaryotic flagella, and the two terms are often used interchangeably. In general, though, the term cilia is used when they are numerous, short and coordinated while flagella is used when they are relatively sparse and long. The name cilium may also be used to emphasize their differences from bacterial flagella.

Cilia are found in all animals, although nematodes and arthropods only have non-motile cilia on some sensory nerve cells. Cilia are rare in plants occurring most notably in cycads. Protozoans (ciliates) possess motile cilia exclusively and use them for either locomotion or to simply move liquid over their surface. Most other organisms that have motile cilia use them only to move liquid over their cell's surface.

Motile cilia are almost never found alone, usually being present on a cell's surface in large numbers that beat coordinately in unified waves. In humans, for example, motile cilia are found in the lining of the trachea or windpipe, where they sweep mucus and dirt out of the lungs. In the oviducts, the beating of cilia moves the ovum from the ovary to the uterus.

Opposite to the motile cilia, non-motile cilium usually exists as one cilium per cell. The outer segment of the rod photoreceptor cell in the human eye is connected to its cell body with a specialized non-motile cilium. The terminal fiber of the olfactory neuron is also a non-motile cilium, where the odorant receptors locate. Almost all types of the mammalian cells have a single non-motile cilium called "Primary cilium" that has been neglected for a long time. Recent studies led scientists to re-evaluate its physiological role(s) in the cell signaling and the control of cell growth and development.

A cilium has an outer membrane that surrounds a core called an axoneme, which contains nine pairs of microtubule doublets and other associated proteins. Motile cilia have a central core with two additional microtubule singlets and dynein motor proteins which are attached to the outer microtubule doublets. Biologists refer to this organization as a cononical "9 + 2" structure. The non-motile cilia do not have the two central microtubule singlets and do not have dyneins. This configuration of axoneme is referred as a "9 + 0" type. At the base of the cilium is its microtubule organization center called a basal body. Basal body is structurally identical to and functionally interchangeable with centriole in the animal cells. The region between the basal body and axoneme is a short transition zone which is less studied.

A defect in the cilium can cause human disease. The best known cilia-related disorder is Primary Ciliary Dyskinesia (PCD). In addition, a defect of the primary cilium in the renal tube cells can lead to polycystic kidney disease (PKD). In another genetic disorder called Bardet-Biedl syndrome (BBS), the mutant gene products are the components in the basal body and cilia.