This study included four dog groups (group A: 10 healthy dogs, group B: 9 dogs with idiopathic epilepsy receiving antiepileptic medication-AEM, group C: 8 dogs with idiopathic epilepsy without AEM administration and group D: 7 dogs with seizures due to structural brain abnormalities). The epileptic dogs were allocated into these 3 groups after a diagnostic investigation that included laboratory testing, thoracic radiographic and abdominal ultrasonographic examination, brain imaging, CSF routine and proteomic analysis. The purpose of the current study was to investigate and compare the proteomic profile among the four groups of dogs.