A primary cilium is a solitary slender non-motile protuberance of structured microtubules (9+0) enclosed by plasma membrane 1 . Housing components of the cell division apparatus between cell divisions, they also serve as specialized compartments for calcium signaling 2 and Hedgehog (Hh) signaling pathways 3 . Specialized sensory cilia such as retinal photoreceptors and olfactory cilia employ diverse ion channels 4- 7 . An ion current has been measured from primary cilia of kidney cells 8 but the responsible genes have not been identified. The polycystin proteins (PC, PKD), identified in linkage studies of polycystic kidney disease 9 , are candidate channels divided into two structural classes: 11-transmembrane (TM) proteins (PKD1, PKD1-L1 and PKD1-L2) remarkable for a large extracellular N-terminus of putative cell adhesion domains and a GPCR proteolytic site, and the 6-TM channel proteins (PKD2, PKD2-L1, PKD2-L2; TRPPs). Evidence suggests that the PKD1s associate with the PKD2s via coiled-coil domains 10- 12 . Here, we employ a transgenic mouse in which only cilia express a fluorophore and employ it to directly record from primary cilia and demonstrate that PKD1-L1 and PKD2-L1 form ion channels at high densities in several cell types. In conjunction with the companion manuscript 2 , we show that the PKD1-L1/PKD2-L1 heteromeric channel establishes the cilia as a unique calcium compartment within cells that modulates established Hedgehog pathways.