Ciliopathies are a rapidly growing group of congenital disorders. Approximately 30% of ciliopathies can be defined primarily by their craniofacial phenotype. Of those disorders, approximately 70% present with midfacial defects, specifically midfacial widening, indicative of increased Hedgehog function. Interestingly, ciliopathies also present with lower jaw defects, specifically micrognathia, indicative of decreased Hedgehog function. Using genomic and biochemical assays we aim to identify ciliary-dependent, prominence-specific mechanisms of Hh pathway regulation during craniofacial development.