Several potassium channel genes have been implicated in epilepsy. We have 
investigated three such genes, KCNJ3, KCNJ6 and KCNQ2, by association studies 
using a broad sample of idiopathic generalised epilepsy (IGE) unselected by 
syndrome. One of the two single nucleotide polymorphisms (SNPs) examined in one 
of the inward rectifying potassium channel genes, KCNJ3, was associated with IGE 
by genotype (P=0.0097), while its association by allele was of borderline 
significance (P=0.051). Analysis of the different clinical subgroups within the 
IGE sample showed more significant association with the presence of absence 
seizures (P=0.0041) and which is still significant after correction for multiple 
testing. Neither SNP in the other rectifying potassium channel gene, KCNJ6, was 
associated with IGE or any subgroup. None of the three SNPs in the voltage-gated 
potassium channel gene, KCNQ2, was associated with IGE. However, one SNP was 
associated with epilepsy with generalised tonic clonic seizures only (P=0.016), 
as was an SNP approximately 56 kb distant in the closely linked nicotinic 
acetylcholine gene CHRNA4 (P=0.014). These two SNPs were not in linkage 
disequilibrium with each other, suggesting that if they are not true 
associations they have independently occurred by chance. Neither association 
remains significant after correcting for multiple testing.