Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder characterized by the presence of multiple cysts in kidneys. ADPKD has been shown to be caused by mutations in the genes of PKD1 and PKD2, encoding polycystin-1 (PC1) and polycystin-2 (PC2), respectively. Polycystins are localized in primary cilia that play roles in multiple biological processes including mechanoreception, Ca2+ influx and cell signalling pathways. Primary cilia are known to play important roles in regulating craniofacial development and growth. In this chapter, we summarize the function of Pkd1 and Pkd2 in controlling mouse craniofacial development and growth, and discuss PKD-associated molecular mechanisms.