Mice homozygous to the partial loss-of-function Dnah5 allele, a component in the ependymal motile cilia, developed congenital hydrocephalus. Volumetric analysis showed enlarged aqueduct, indicating that the hydrocephalus was not caused by collapsed aqueduct, but rather by altered cerebrospinal fluid homeostasis. Furthermore, specific brain regions displayed dysplasia, including hippocampus, olfactory bulb and cerebellum. Diffusion tractography followed by topology analysis showed altered neuronal network organization in these brain areas. Our study suggests that ependymal cilia may play a crucial role in grey matter and white matter development and neuronal network organization.