A logical first place to look in order to identify loci determining behavioral differences between inbred and certain outbred strains of mice is among the proteins expressed in brain. Fourteen mouse brain proteins have been demonstrated to be genetically variant, four of these have been chromosomally mapped and an additional twelve have been identified and can be simultaneously screened by two dimensional electrophoresis. Certain genetic differences in behavior relevant to alcohol consumption and the effects of alcohol occur between inbred, recombinant inbred and selectively outbred strains. Two genetic correlations are reported, one between an isoelectric point variant of A7 (a 71 kd, pI 5.4 abundant protein) and resistance to signs of ethanol withdrawal and the other between A12 (a 28 kd, pI 5.6 protein) and ethanol intake. Though tentative, these findings illustrate the power of this approach for behavioral genetic analysis and may allow the biochemical genetic bases of these traits to be understood.