Antidepressants are widely used for the treatment of psychiatric disorders, including depression and anxiety. Although they are efficient drugs, there are several unsolved questions regarding their clinical pharmacology. Furthermore, the molecular mechanisms of action of antidepressants are still poorly understood and the molecular targets and pathways remain to be identified. To address these issues, we performed a gene expression analysis in mice treated with two commonly used antidepressants with differing pharmacology (paroxetine or mirtazapine) for 1, 7 or 28 days. We quantified the effects of these treatments on gene expression in the mouse brain with cDNA-microarrays containing 3624 expressed sequence tags (ESTs) representing murine genes expressed in the brain. We found that both drugs led to downregulation of four common genes. In addition, although it was possible to identify common targets for the two drugs, the expression profiles of the drugs differed in a fundamental manner, and the longer the treatment duration, the greater the difference in the profiles. These findings suggest that antidepressants with different pharmacologies can share molecular targets even though the primary pathways at which they act are different.