Repeated exposure to ethanol in mice induces behavioural sensitization, a progressive increase in locomotor activity that is common to drugs of abuse. Not all mice however show sensitization to ethanol. The goal of the present study was to examine whether variability in the sensitization response to ethanol (EtOH) is differentially associated with regional brain changes in specific molecular markers associated with neuroplasticity, namely BDNF and its receptor trkB, and levels of phosphorylated cyclic AMP-regulated element-binding protein (pCREB), 14 days after withdrawal from chronic, intermittent EtOH exposure. Male DBA/2NCrl mice received 7 biweekly EtOH (2.2g/kg, i.p.) or saline (SAL) injections and were classified as Sensitized or Non-sensitized on the basis of final locomotor activity (LMA) scores. Brains were removed two weeks later for immunohistochemical and in situ hybridization analyses. Compared to SAL-treated and Non-sensitized mice, Sensitized animals showed a higher number of pCREB-immunoreactive cells in the nucleus accumbens shell (+68% and +50%, respectively) and in the bed nucleus of the stria terminalis (+61% and 46%, respectively), whereas SAL and Non-sensitized groups did not differ from each other. A different pattern was seen when BDNF and trkB mRNA levels were analyzed in the same groups. Non-sensitized mice displayed lower BDNF mRNA in several brain areas and significantly lower trkB levels throughout the brain when compared to either the Sensitized or to SAL groups, which did not differ from each other. These results indicate that sensitization to EtOH is differentially associated with increased pCREB levels in specific brain areas. The observed decrease in BDNF and trkB mRNA in the Non-sensitized group suggests the possibility that EtOH may have neurotoxic effects in a subpopulation of mice, which might in turn prevent the development of behavioural sensitization. The lack of a difference in BDNF and trkB mRNA expression between Sensitized and SAL mice suggests that EtOH sensitization may be mediated by mechanisms different from those mediating sensitization to other psychostimulants.