The DBA/2J (D2) and C57BL/6J (B6) mouse strains are the most widely studied genetic models of severe and mild acute alcohol withdrawal, respectively. Previous studies have identified quantitative trait loci and genes involved in risk for acute ethanol withdrawal using mapping populations derived from the D2 and B6 strains, but the brain region(s) and circuit(s) by which these genes and their protein products influence ethanol physiological dependence and associated withdrawal remain to be elucidated.B6 and D2 were administered a sedative-hypnotic dose of ethanol (4 g/kg) or saline (control) and returned to their home cages where they were left undisturbed for 7 hr, which has been shown in previous studies to correspond to peak acute ethanol withdrawal severity. The mice were then euthanized and assessed for their numbers of c-Fos immunoreactive neurons across 26 brain regions. The question addressed was whether or not ethanol-withdrawn D2 and B6 mice differed in c-Fos induction (neural activation) within circuitry that could explain the severe ethanol withdrawal of the D2 strain and the mild ethanol withdrawal in B6 strain mice.At peak acute ethanol-withdrawal ethanol-withdrawn D2 and B6 mice differed in neural activation within the basal ganglia, including the subthalamic nucleus and the two major output nuclei of the basal ganglia (the medial globus pallidus and the substantia nigra pars reticulata). Genotype-dependent c-Fos induction was also apparent in associated circuitry including the lateral septum, the ventral tegmental area, the nucleus accumbens core, the dorsolateral caudate putamen, the substantia nigra pars compacta, the cingulate and entorhinal cortices, and the ventral pallidum. D2 and B6 mice showed comparable neural activation in the bed nucleus of the stria terminalis, and the nucleus accumbens shell.The present studies are the first to use immediate early gene product expression to assess the pattern of neural activation associated with acute ethanol withdrawal. Our results point to the involvement of an extended basal ganglia circuit in genetically determined differences in acute ethanol withdrawal. Based on these data, we suggest that quantitative trait genes (QTGs) involved in acute ethanol withdrawal exert their effects on this phenotype via one or more of the brain regions and circuits identified. As more information becomes available that integrates neural circuit and QTG analyses, the precise mechanisms by which QTGs affect ethanol physiological dependence and associated withdrawal will become apparent.