Abnormalities of deep cerebellar nuclei in Joubert syndrome have been previously reported only in rare autopsy cases. Epilepsy in association with Joubert syndrome is also rarely reported. In two new cases of patients with Joubert syndrome, bilateral hypoplasia of deep cerebellar nuclei was detected in vivo by magnetic resonance imaging. One of the patients had drug-resistant epilepsy. Both patients received clinical examination, electroencephalography, neuropsychologic testing, and high-resolution magnetic resonance imaging (1.5 T). Patient 1, a 7-year-old boy, had muscular hypotonia, periodic tachypnea, mild ataxia, global developmental delay, exotropia, and polydactyly. Patient 2, a 23-year-old woman, had muscular hypotonia, epilepsy with pharmacoresistant generalized tonic-clonic seizures, learning disability, esotropia, and mild gait ataxia. Abnormalities of deep cerebellar nuclei might contribute to the pathophysiology of epilepsy in patients with Joubert syndrome.