Stress refers to physiological or psychological stimuli that disrupt homeostasis and induce pathophysiological conditions due to maladaptive response, sometimes resulting in mental disorders including depression and post-traumatic stress disorder. Severe stress has been shown to induce neuronal atrophy and apoptosis, especially in the hippocampus, which is thought to be a region of the brain important in stress-related disorders. We have analyzed gene expression in rat hippocampus comprehensively to clarify the molecular mechanism of stress-related disorders. In the present study, we identified and catalogued 13,660 partial complementary DNA sequences (expressed sequence tags (ESTs)) of randomly selected clones from a cDNA library of rat hippocampus. Sequence analysis showed that these clones cluster into 7173 non-redundant sequences comprising 1794 clusters and 5379 singletons. As a result of nucleotide and peptide database search, 2594 were found to represent known rat sequences. Of the remaining 4579 genes, 599 non-redundant ESTs represent rat homologs of genes identified in other species or new members of structurally related families. In addition, we illustrate the use of these clone sets by constructing a cDNA microarray focused on genes categorized into "cell/organism defense". These ESTs and our own microarray thus provide an improved genomic source for molecular studies of animal models of stress-related disorders.