DNA microarray analysis was used to identify candidate ethanol-regulated genes, as a first step towards exploring how transcriptional changes might lead to ethanol-induced changes in behaviour. Mice were treated with a single acute intraperitoneal ethanol dose and DNA microarray analysis performed on midbrain 2 h posttreatment. We predicted that if ethanol-regulated genes contribute towards behaviour, then constitutive variation in brain expression levels may also contribute to strain-specific differences in ethanol-related behaviour of inbred mouse strains. On the basis of this assumption, we interrogated the BXD inbred strain phenotype database and the U74Av2 MAS5 brain expression database using the WebQTL tool (http://www.genenetwork.org/) and correlated ethanol-related behaviours to expression levels. Constitutive expression levels of 70/90 candidate genes, identified from the DNA microarray analysis, varied significantly between inbred strains and correlated significantly with strain-specific differences in ethanol-related behaviours. These genes were then mapped onto biochemical pathways using Stratagene's PathwayAssist software. This analysis identified the transcription factor Sp1 and NFκB pathways in the acute response to ethanol. Ethanol regulation of Sp1 transcription was conserved between humans and mouse. As predicted, downstream targets of Sp1 were also ethanol regulated. NFκBia, an important regulator of NFκB function and Rela, an NFκB-binding partner, were both regulated by ethanol. Expression of both Sp1 and NFκBiα were also downregulated following chronic ethanol treatment. As Sp1 and NFκB are implicated in plasticity and behaviour, our data suggest a role for these transcription factors in the long-term behavioural adaptations to ethanol.