The Lewis (LEW) and Fischer 344 (F344) rat strains are widely used as models of genetic vulnerability to drug addiction, particularly since these two strains show different patterns of drug selfadministration. We previously performed an unbiased and genomewide microarray analysis to define the differences in gene expression in the nucleus accumbens (NAcc) and prefrontal cortex between LEW and F344 rats. In this study, we set out to determine the strain differences in the NAcc and amygdala at the protein level using bidimensional gel electrophoresis. As such, 11 proteins were found to be differentially expressed between these two strains, the activity of which was mainly related to vesicular trafficking (STXBP1 and GDI1), energy metabolism (ATP5B, ENO2, and ACOT7), and cytoskeletal formation. This information might be useful to search for new molecular targets to screen individuals at high risk of developing an addictive disorder.