Objective: Mutations in the CLN3 gene lead to juvenile neuronal ceroid lipofuscinosis, a pediatric neurodegenerative disorder characterized by visual loss, epilepsy and psychomotor deterioration. Although most CLN3 patients carry the same 1 kb deletion in the CLN3 gene, their disease phenotype is variable. The aims of this study were to identify (1) genes which are dysregulated in CLN3-disease regardless of the clinical course and could act as new biomarkers, and (2) modifier genes which may affect the progression of the disease delaying deterioration.