Joubert syndrome is a rare genetic neurologic disorder associated with hypoplasia or absence of the cerebellar vermis. The classic form is characterized by ataxia, hypotonia, eye movement abnormalities, developmental delay, and abnormal breathing patterns. In contrast, other patients have the additional feature of kidney cysts. This population could represent a distinct form of Joubert syndrome. One case of Joubert syndrome with subcortical neuroepithelial cysts was recently described. We report a new case of Joubert syndrome with overlapping features, including diffuse progressive central nervous system neuroepithelial cysts and kidney cysts. Our data suggest that neuroepithelial cysts occur in conjunction with Joubert syndrome associated with kidney cysts.