OBJECTIVE To describe recent research focusing on the analysis of gene and protein expression relevant to understanding ethanol consumption, dependence and effects, in order to identify common themes. METHODS A selective literature search was used to collate the relevant data. RESULTS Over 160 genes have been individually assessed before or after ethanol administration, as well as in genetically selected lines. Techniques for studying gene expression include northern blots, differential display, real time reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization. More recently, high throughput functional genomic technology, such as DNA microarrays, has been used to examine gene expression. Recent gene expression analyses have dramatically increased the number of candidate genes (nine array papers have illuminated 600 novel gene transcripts that may contribute to alcohol abuse and alcoholism). CONCLUSIONS Although functional genomic experiments (transcriptome analysis) have failed to identify a single alcoholism gene, they have illuminated important pathways and gene products that may contribute to the risk of alcohol abuse and alcoholism.