The ciliopathies are a rare class of human genetic disorder caused by dysfunction of the primary cilium in development and adulthood. This work investigates several novel elements of these diseases. Using advanced image analysis, facial dysmorphology in patients with ciliopathies is characterised and modelled in zebrafish. This uncovers a new role for ciliopathy proteins in cell migration, and furthermore in Sonic Hedgehog signalling. The zebrafish is used to model the renal component of ciliopathies and a therapeutic assay is developed to test the efficacy of drugs to treat renal cysts. Together, these findings have contributed to the diagnosis and potential treatments for ciliopathies.