Benign partial epilepsy with centrotemporal sharp waves (benign rolandic epilepsy, BRE) is a common form of idiopathic, localisation-related epilepsy of childhood. The characteristic age-dependent focal sharp wave (fsw) found on the EEG in this disorder segregates as an autosomal dominant trait in families with probands with BRE and acts as a neurobiological marker for the increased risk of developing BRE, other benign partial epilepsies of childhood, and other developmental disorders in these families. One of the genes for idiopathic generalised epilepsy (IGE), designated EJM1, has been mapped in families with probands with juvenile myoclonic epilepsy, by linkage to the HLA region on chromosome 6. As BRE and IGE are benign, idiopathic, age-dependent epilepsies, EJM1 is a candidate locus for the fsw underlying BRE and related disorders. Genetic linkage analysis was undertaken in 11 families with probands with BRE and one or more first degree relatives with fsw, with or without BRE, using a polymorphic DNA marker within the HLA region. Apparently unaffected individuals were classed as affection status unknown. Assuming autosomal dominant inheritance with a penetrance of 0.9 gave a lod score of -2.3 at zero recombination, excluding the candidate gene region around HLA. These observations exclude an important candidate gene for this common disorder, and suggest a fundamental molecular and genetic distinction between the benign partial epilepsies of childhood and the idiopathic generalised epilepsies.