Primary cilia are essential organelles mediating key cell signaling activities. The molecular architecture of primary cilia remains largely unknown, hindering our understanding in ciliogenesis, cilium-mediated signaling, and cilium-associated cellular activities. Superresolution microscopy fits the need in revealing the structure and functions of ciliary proteins. We have used superresolution microscopy to determine the molecular architecture of the transition zone at the ciliary base. We are now working on mapping the molecular architecture of other regions of primary cilia such as the distal appendages.