Different rat strains exhibit large differences in hypothalamic pituitary-adrenal activity that have been used to determine the role of the neuroendocrine system in susceptibility to autoimmune disease. To further characterize potential behavioral correlates of these differences, the amplitude of the acoustic (ASR) and tactile (TSR) startle response and the corticosterone response to acoustic startle stimuli were compared between two histocompatible strains, Lewis (LEW/N) and Fischer (F344/N) rats, as well as outbred Harlan Sprague-Dawley (SD) rats. Startle stimuli elicited larger ASR and TSR in LEW/N rats than in F344/N rats, with SD rats exhibiting an intermediate response. The ASR habituated at a similar rate in LEW/N and F344 rats, while the ASR did not habituate in SD rats. After handling and placement in the startle chambers, the three strains did not differ in control levels of corticosterone. In contrast, exposure to acoustic startle stimuli increased corticosterone 5-fold in F344/N rats and 2-fold in SD rats, but had no effect on corticosterone in LEW/N rats. These findings suggested an inverse relationship between the amplitude of the ASR and hypothalamic-pituitary-adrenal activation across strains. This relationship was further supported by a high negative correlation between corticosterone level and ASR amplitude within the F344/N group.