The primary cilium, made up of microtubules, acts as antennae on the cell surfaces for relaying external stimuli into the cells. These fine hair-like structures are present, generally one per cell. These are non-motile cilia in a 9+0 microtubules arrangement, where the central pair of microtubules are absent. The primary cilia arise from the basal body embedded in the cell membrane. Intraflagellar transport (IFT) carries requisite proteins from the cytoplasm to the cilium because the primary cilium cannot synthesize proteins. These are resistant to microtubule disassembly-causing drugs like colchicine.

The primary cilium plays a role in several key signaling pathways, among which the calcium-dependent signaling pathway has been most widely studied. However, recent studies have highlighted their roles in calcium-independent pathways like Sonic-hedgehog, Wnt, PDGFR, Notch, etc.

In humans, the primary cilium, although found in almost all cell types, but is most common in epithelial cells. They have a key role in the node of the vertebrate, which is responsible for positioning the organs in the developing embryo. The primary cilium moves in a circular motion to create the left-right symmetry for the correct positioning of the visceral organs. A defect in genes responsible for forming primary cilium results in the sinus invertus disorder, where the typical symmetry of the organs in the embryo is lost. Other diseases associated with the defect in primary cilium include Meckel-Guber syndrome, Bardet-Beedle syndrome, polycystic kidney disorder, and Joubert syndrome.