The purpose of this study was to determine whether exercise training changes the extent or pattern of activation of areas in the central nervous system (CNS) involved in cardiorespiratory control. Rats that spontaneously trained on running wheels for 80-100 days were compared to rats that were not provided an opportunity to exercise. Selected brain regions including the hypothalamic and mesencephalic locomotor regions, and ventrolateral medulla were studied using c-Fos-like immunocytochemistry. A single test bout of exercise evoked significantly less activation as indicated by Fos labeling in the posterior (caudal) hypothalamic area, periaqueductal gray, nucleus of the tractus solitarius and the rostral ventrolateral medulla of the trained rats when compared to sedentary rats. These results are consistent with the concept that the nervous system changes its responses to a given level of exercise after training. These changes may also be related to perceived exertion.