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Several lines of evidence indicate that adverse experience in early life may be a triggering factor for disturbances in the brain mitochondrial proteins and lead to the development of depression in adulthood. On the other hand, little is known about the impact of chronic administration of various antidepressant drugs on the brain mitochondria, as a target for the pharmacotherapy of depression.The purpose of our study was to compare the impact of chronic treatment with two antidepressant drugs with different mechanisms of action, a tricyclic antidepressant (TCA), imipramine, and an antidepressant of the selective serotonin reuptake inhibitor (SSRI) class, fluoxetine, on the mitochondria-enriched subproteome profile in the hippocampus of 3-month-old male rats following a prenatal stress procedure (an animal model of depression).We clearly confirmed that chronic imipramine and fluoxetine administration not only normalized depression-like disturbances evoked by the prenatal stress procedure but also modulated the mitochondria-enriched subproteome profile in the hippocampus of adult offspring rats. In line with this, two-dimensional electrophoresis coupled with mass spectrometry showed a statistically significant down-regulation of 14–3–3 and cytochrome bc1 proteins and an up-regulation of COP9 signalosome expression after chronic imipramine treatment in the hippocampus of prenatally stressed offspring. Fluoxetine administration strongly up-regulated the expression of cathepsin D, one of the key proteins involved in the prevention of the development of neurodegenerative processes. Furthermore, this antidepressant treatment enhanced expression of proteins engaged in the improvement of learning and memory processes (STMN1, Dnm-1) as well as in mitochondrial biogenesis and defense against oxidative stress (DJ-1).These findings provide new evidence that chronic administration of antidepressants exerts a varied impact on the mitochondria-enriched subproteome in the hippocampus of adult rats following a prenatal stress procedure. In particular, the effect of fluoxetine requires additional experiments to elucidate the possible beneficial biological consequences underlying the effects mediated by this antidepressant.Chronic administration of antidepressant drugs exerts a varied impact on the mitochondrial proteins in the hippocampus of stressed rats.Fluoxetine administration strongly up-regulates the expression of proteins involved in multidirectional processes.The mitochondrial effect evoked by imipramine treatment in hippocampus seems to be limited.