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We used transcranial magnetic stimulation to investigate whether the cortical excitability changes observed amongst the different generalized and focal epilepsy syndromes are reflected in their asymptomatic siblings and if these changes depended on the clinical phenotype. We studied 157 patients with epilepsy (95 generalized and 62 focal) and their asymptomatic siblings (138 and 82, respectively). Motor threshold and paired pulse transcranial magnetic stimulation at short (2, 5, 10 and 15 ms) and long (100–300 ms) interstimulus intervals were measured. Results were compared to those of 12 control subjects and 20 of their siblings. There were no differences in cortical excitability between healthy control subjects and their siblings. Compared with control subjects, cortical excitability was higher in siblings of patients whether generalized (P < 0.05; short and long interstimulus intervals) or focal (P < 0.05; long interstimulus intervals). Compared with epilepsy, motor threshold was lower (P < 0.05) in patients with juvenile myoclonic epilepsy compared with their siblings only early at onset in the drug naïve state. In all groups (generalized and focal) cortical excitability was lower in siblings only at the long interstimulus intervals (250 and 300; P < 0.05). Cortical excitability is higher in asymptomatic siblings of patients with generalized and focal epilepsy in a similar manner. The disturbance seems to involve intracortical inhibitory circuits even in the siblings of patients with a structural abnormality (acquired epilepsy). This implies there are certain genetic factors that predispose to both generalized and focal epilepsies and a complex genetic/environmental interaction then determines the clinical phenotype.