We report on an 11-year-old boy with familial juvenile nephronophthisis type I associated with cerebellar ataxia and nystagmus, but not with ocular motor apraxia. An MRI revealed hypoplasia of the brainstem and vermis, and an enlargement of the fourth ventricle. A molecular genetic analysis demonstrated a homozygous deletion including the NPHP1 gene. These findings suggest that NPHP1 may play an important role in the normal development of the brainstem and the cerebellum as well as renal tissue.