Whilst the effects and associated costs of excessive alcohol consumption in the human population are obvious at one level, the roles played by genetic factors at the molecular level are still unclear. Drosophila melanogaster has an alcohol response comparable to humans and is used as a genetic model to study the functional roles of genes regulated in response to ethanol. In the current study, the biological processes associated with behavioural responses to acute alcohol exposure in Drosophila have been analysed using whole genome expression profiling. Ethanol response genes differentially expressed (a) at a single time point (2 h) and (b) in a time series (0-4 h) were identified using microarrays. In addition, a subset of differentially expressed genes was validated using behavioural sedation and recovery assays. The study shows that genes involved in redox processes, neuron development, and specific signalling and metabolic pathways (including glutathione metabolism) form part of the response to ethanol in Drosophila. Biological processes for the regulation of oxidative stress are the common functional denominator of many of the ethanol response genes identified. These upregulated genes work to rescue cells from oxidative stress and its consequences such as protein misfolding, apoptosis and ageing. In the current study, an enrichment of Drosophila genes linked to ageing is observed for the first time. The functional genomics data revealed by such studies can be used to predict transcription networks of ethanol response genes, but the future lies in mapping these networks to the human population, with the ultimate aim of identifying genetic factors for alcohol use disorders.