The present study has employed quantitative receptor autoradiography and in situ hybridisation histochemistry to compare the expression of the mRNA encoding the alpha 1 and alpha 2 subunits of the GABAA receptor and the binding density of mature GABAA receptors in the limbic system of alcohol-preferring Fawn-Hooded rats (FH) with Wistar-Kyoto rats (WKY). Quantifiable levels of mRNA encoding the alpha 1 subunit were found in cortical regions, ventral pallidum, substantia nigra, horizontal limb of the diagonal band and the hippocampus of both rat strains. Interestingly, expression of the alpha 1 subunit mRNA was decreased by approximately 30% in the hippocampus of FH compared to WKY rats. Following a 28-day period with free access to 10% ethanol, expression of the alpha 1 subunit transcript, was significantly increased in the piriform cortex and horizontal limb of the diagonal band, unaltered in the hippocampus but decreased in the substantia nigra of FH rats. Quantifiable levels of mRNA encoding the alpha 2 subunit were found in nucleus accumbens, amygdala, cortical regions, lateral septal nucleus, hippocampus, medial habenula and ventral pallidum of both strains. Expression of the alpha 2 subunit mRNA was decreased by approximately 35% in both the hippocampus and occipital cortex of FH compared to WKY rats. However, consumption of 10% ethanol in FH rats had no impact upon expression of the mRNA encoding the alpha 2 subunit in any region examined. Mature GABAA receptors were studied by autoradiography utilising the antagonist radioligand [3H]SR95531 and the agonist radioligand [3H]muscimol. Topographic binding throughout the limbic system of both strains was observed for both radioligands. Specifically, [3H]SR95531 binding was higher in the occipital cortex, hippocampus, lateral septal nucleus, superior colliculus and ventral pallidum of the FH rats compared to WKY rats; however, in the nucleus accumbens [3H]SR95531 binding was lower in FH compared to WKY. Ethanol consumption had no measurable effect on the binding of [3H]SR95531 in FH rats. In the case of [3H]muscimol, binding was higher in the cortex, lateral septum and ventral pallidum of FH compared to WKY. Furthermore, ethanol consumption resulted in a 25-30% increase in [3H]muscimol binding in the lateral septum and striatum of FH rats. These data provide evidence for differential expression of GABAA receptor subunits in FH and WKY rats, and additionally indicate anatomically defined variations in GABAA receptor binding between the two rat strains.