Here, we report that suppression of apical phosphatidylinositol 4,5- bisphosphate [PtdIns(4,5)P<sub>2</sub>], by overexpressing apically targeted PtdIns(4,5)P<sub>2</sub> phosphatase or by knocking down type I phosphatidylinositol 4-phosphate 5-kinase (Pip5k1), leads to ciliogenesis defects and polycystic kidney disease (PKD) in zebrafish embryos that phenocopied inpp5e mutant, a Joubert syndrome model.