We studied changes in the stability of the genome in cells of two brain regions (prefrontal cortex and hippocampus), as well as in the bone marrow of rats with a hereditary high and low thresholds of excitability of the nervous system (strains HT and LT, respectively) after prolonged exposure with emotional-pain stressor. To study the reactivity of the brain cells genome, phosphorylated histone γ-H2AX (γ-H2AX phospho Ser139) was used. The level of mitotic disturbances in bone marrow cells was also assessed. Between the animals of the control groups, there were no interstrain differences in the studied parameters. Stress exposure increases the immunoreactivity to γ-H2AX phospho Ser139 of the prefrontal cortex cells and the level of chromosomal aberrations in bone marrow cells in animals of both strains. In cells of the dentate gyrus of the hippocampus, a specific increase in immunoreactivity to γ-H2AX phospho Ser139 was revealed in rats of the low-excitable HT strain. The relationship between the reaction of cells of this zone of hippocampus to the stressor exposure with the hereditary level of excitability of the nervous system of animals is discussed.