We have established that the GABA(A) receptor alpha(6) (Gabra6) and alpha(1) (Gabra1) subunit genes are tightly linked on mouse chromosome 11 by analyzing the strain distribution patterns of RFLPs for the two genes and microsatellite markers flanking these genes in 26 BXD recombinant inbred strains. These results further demonstrate clustering of the GABA(A) receptor subunit genes on mouse chromosomes and the synteny for these clusters between the mouse and human genomes.