Most experimental approaches to studying complex traits such as AUD have focused on identifying the role for “single genes” even when employing genome-wide tools such as microarrays. More recently, microarray expression data has been used in systems genetics studies to construct maps of gene interactions on the basis of correlated expression patterns, providing unprecedented insight into the molecular networks underlying complex traits. Such network-based approaches may prove to be more effective for delineating genetic factors underlying individual variation in AUD risk and the neurobiology of ethanol and drug abuse disorders. A gene network (a group of genes that are coordinately regulated or functionally inter-related) producing significant influence on neural pathways affecting ethanol-associated behaviors is both more likely to be experimentally detected across human and animal studies and may also identify key nodes that could serve as rationale therapeutic targets.