The interaction between the cerebellum and cerebrum forms the anatomic basis of the cerebellar role in neurocognitive functions. We performed whole-brain atlas-based analysis of volumetric and DTI data in a 16-month-old boy with Joubert syndrome and 5 age-matched controls. In our patient, we found a decrease in volume of multiple gray and white matter regions, and reduced fractional anisotropy in selected white matter regions. These findings result from trophic trans-synaptic effects and disconnection of the cerebellar-cerebral pathway secondary to a malformed cerebellum. In addition, we found an increase in fractional anisotropy in multiple cortical gray matter regions, which may reflect disrupted cortical neuronal radial glial cell scaffolding and neuronal laminar organization.