Development of novel therapies for polycystic kidney disease (PKD) requires assays that adequately reflect disease biology, and are adaptable to high throughput screening. Here we describe an embryonic cystic kidney organ culture model, and demonstrate that a new mutant allele of the Pkd1 gene (Pkd1^tm1Bdgz) modulates cystogenesis in this model. Cyst formation induced by cAMP is influenced by the dosage of the mutant allele: Pkd1^tm1Bdgz -/- cultures develop a larger cystic area compared to +/+ counterparts, while Pkd1^tm1Bdgz +/- cultures show an intermediate phenotype. A similar relationship between the degree of cystogenesis and mutant gene dosage is seen in cystic kidney organ cultures derived from mice with a mutated Nek8 gene (Nek8^jck). Both Pkd1- and Nek8-cultures display altered cell-cell junctions, with reduced E-cadherin expression and altered desmosomal protein expression, similar to ADPKD epithelia. Additionally, characteristic ciliary abnormalities are identified in cystic kidney cultures, with elevated ciliary polycystin 1 expression in Nek8 homozygous cultures, and elevated ciliary Nek8 protein expression in Pkd1 homozygotes. These data suggest that the Nek8 and Pkd1 genes function in a common pathway to regulate cystogenesis. Moreover, compound Pkd1 and Nek8 heterozygous adult mice develop a more aggressive cystic disease than animals with a mutation in either gene alone. Finally, we validate the kidney organ culture cystogenesis assay as a therapeutic testing platform using the CDK inhibitor roscovitine. Therefore, embryonic kidney organ culture represents a relevant model for studying molecular cystogenesis and a rapid tool to screen for therapies that block cystic growth.