Animal models represent a very useful tool for the study of depressive-like behavior and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated with human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in three animal models of depression: acute treatment with reserpine, olfactory bulbectomy and chronic treatment with corticosterone. Gene expression analysis was carried out using the Affymetrix GeneChip® technology. The results were evaluated using the GeneChip Operating software (Gcos 1.3) and analyzed with the GeneSpring GX v7.3 bioinformatics software (Agilent) and dChip 2005 software. Expression changes were validated with quantitative real-time polymerase chain reaction (RT-PCR) assays. Many transcripts were differentially expressed in the cortex of depressed-like animals in each model. Gene ontology analysis showed that significant gene changes were clustered primarily into functional neurochemical pathways associated with apoptosis and neuronal differentiation. When expression profiles were compared among the three models, the number of transcripts differentially expressed decreased and only two transcripts (complement component 3 and fatty acid-binding protein 7) were differentially expressed in common. Both genes were validated with RT-PCR. Moreover, five (Htr2a, Ntrk3, Crhr1, Ntrk2 and Crh) of the genes classically related to human major depression were differentially expressed in at least one of these models. The different animal models of depression share relevant characteristics although gene expression patterns are different among them. Moreover, some of the classical genes related to human major depression are differentially expressed in these models.