Ethanol is an addictive drug that deteriorates different neuronal pathways in the CNS, leading to the induction of cognitive dysfunction. Neuroimaging analyses revealed that alcohol-induced brain damage appears to be region-specific and major dysmorphology has been observed in the prefrontal cortex and the white matter (WM) particularly in the corpus callosum (CC). Recent diffusion tensor imaging (DTI) analysis indicated that microstructural degradation was prominent in the genu followed by the body and the splenium of the CC. Molecular mechanisms underlying these structural changes are largely unknown. In this study, using 2D electrophoresis based proteomics approach, protein expression profiles in 25 genus samples (12 controls, 7 uncomplicated alcoholics and 6 complicated alcoholics with hepatic cirrhosis) were analysed and compared. Image analysis showed that 35 protein spots in the uncomplicated alcoholic and 56 in the complicated group were differentially altered compared to the control (P<0.05; ANOVA). In total of 91 spots, 25 spots were overlapped between two alcoholic groups. When protein expression profile of the genu was compared with those in other WMs [BA9 white matter (WM) and splenium] the highest number of region-specific proteins was identified in the genus indicating that genu might be the most sensitive and/or vulnerable region to chronic alcohol ingestion at least from the aspect of protein expression. Out of total 66 spots (identified as 50 different proteins), 31 spots (identified as 28 different proteins) were expressed only in the complicated group. This result indicates that alcohol-related liver dysfunction has synergetic effects on brain protein expression. It is also interesting to note that abnormality in thiamine-related cascade which was previously found in the BA9 WM was observed in the genu, but not in the splenium. It is therefore suggested that both hepatic and nutritious factors might be underlying the mechanisms of microstructural damage detected by DTI.