In the present study, we investigated whether ethanol physical dependence causes changes of serotonin transporter (SERT) expression in the brain. SERT expression increased in the cingulate cortex, nucleus accumbens, hippocampal CA1-CA3 layers, and mediodorsal nucleus of the thalamus and decreased in the basolateral nucleus of the amygdala. In addition, chronic ethanol treatment increased SERT mRNA in the dorsal raphe nucleus from which serotonergic neurons originate, although no SERT mRNA was detected in the regions where SERT protein increased. These findings suggest that alteration of SERT levels in the brain may be related to emotional changes observed in ethanol physical dependence.