Both linkage and association studies provide strong evidence that a gene locus on chromosome 6 is involved in the expression of juvenile myoclonic epilepsy (JME), an adolescent-onset form of primary idiopathic generalized epilepsy (IGE). This epilepsy-related gene locus, designated EJM-1, may also influence the expression of other forms of IGE. We report here evidence that at least one form of epilepsy that is similar to JME--pure, adolescent-onset grand mal epilepsy in which the seizures occur at any time during waking--is not linked to the EJM-1 locus. However, we also have evidence that another form of pure, adolescent-onset grand mal that occurs on awakening is linked to the EJM-1 locus and may be genetically the same as JME. This work suggests that clinically similar epileptic syndromes may have different genetic bases and underscores the critical importance of careful clinical observations in studying the genetics of the epilepsies.