A cilium (plural cilia) is a fine projection from a eukaryotic cell that constantly beats in one direction. They are structurally identical to eukaryotic flagella, and the terms are often used interchangeably. In general, though, the term cilium is used when they are numerous, short and coordinated while flagellum is used when they are relatively sparse and long. The name cilium may also be used to emphasize their differences from bacterial flagella.

These structures are found in all animalia except arthropods and nematodes. They are rare in plants occurring most notably in cycads. Protozoans with cilia (ciliates) use them for either locomotion or to simply move liquid over their surface. Most other organisms that have cilia use them only to move liquid over their cell's surface. Cilia are almost never found alone, usually being present on a cell's surface in large numbers that beat in unified waves.

In humans, cilia are found for example in the lining of the windpipe, where they sweep mucus and dirt out of the lungs, and in the oviducts, where they move the ovum from the ovary to the uterus.

A cilium has an outer membrane that surrounds a matrix which contains nine microtubules around a central core with two additional microtubules. Biologists refer to this organization as a 9 + 2 structure.