Evidence from the literature suggests that testosterone (T) plays an important role in the neural structure, physiology, and function of the hippocampus (HP). However, many of the genes involved and underlying mechanisms remain to be elucidated. To shed light on this issue, we explored the transcriptome of HP in orchidectomized (OOX) rats to identify T-dependent gene expression in rat HP. RNA from OOX and sham HP animals were processed and measured by the Applied Biosystems microarray platform. The results showed a total of 271 genes differentially expressed between OOX vs. sham animals. Overall, T depletion resulted in the upregulation of 98 genes, including genes associated with neurogenesis and behavior. Of particular interest was the downregulation of 173 genes, with known functions, including signal transduction or neurological system processes. Our data shows that T depletion results in significantly altered hippocampal gene expression profiles and constitutes a starting tool to elucidating the molecular mechanisms involved in the action of androgens in the physiology of the HP.