Distinct mutations in the centrosomal-cilia protein CEP290 lead to diverse clinical findings in syndromic ciliopathies. We show that CEP290 localizes to the transition zone in ciliated cells, precisely to the region of Y-linkers between central microtubules and plasma membrane. To create models of CEP290-associated ciliopathy syndromes, we generated Cep290^ko/ko and Cep290^gt/gt mice that produce no or a truncated CEP290 protein, respectively. Cep290^ko/ko mice exhibit early vision loss and die from hydrocephalus. Retinal photoreceptors in Cep290^ko/ko mice lack connecting cilia, and ciliated ventricular ependyma fails to mature. The minority of Cep290^ko/ko mice that escape hydrocephalus demonstrate progressive kidney pathology. Cep290^gt/gt mice die at mid-gestation, and the occasional Cep290^gt/gt mouse that survives shows hydrocephalus and severely cystic kidneys. Partial loss of CEP290-interacting ciliopathy protein MKKS mitigates lethality and renal pathology in Cep290^gt/gt mice. Our studies demonstrate domain-specific functions of CEP290 and provide novel therapeutic paradigms for ciliopathies.