Background: Exercise stress promoted cortisol and testosterone secretions that have their own circadian rhythms. It is necessary that the testosterone, cortisol and testosterone/cortisol ratio (T/C ratio) are measured through their rhythms for use in monitoring exercise-induced stress in athletes. Automated measurement has not been applied to salivary testosterone, which requires passive drooling difficult to collect sufficient saliva rapidly. This study aimed to verify whether automated measurements of the testosterone and cortisol concentrations and T/C ratio using saliva collected sequentially can effectively assess exercise intensity differences within circadian rhythms in male athletes.Methods: We investigated the correlations of testosterone and cortisol concentrations measured by electrochemiluminescence immunoassay (ECLIA) between saliva and sera collected from 20 male long-distance runners. We collected the runners' saliva sequentially by passive drooling on two consecutive days involving different intensity trainings in the morning and evening; salivary testosterone and cortisol concentrations were measured by ECLIA. Each exercise intensity was measured by running distances, velocities, Borg scale score and maximum pulse rate during exercise.Results: The salivary testosterone and cortisol concentrations were positively correlated with the respective total serum hormone concentrations. The runners were divided into low-intensity exercise group (n = 8) and high-intensity exercise group (n = 7), in which five runners were excluded because measurable saliva samples could not be obtained due to low volume and high-viscosity. Sequential saliva collection and automated measurements detected the runners' circadian rhythms of testosterone, cortisol and T/C ratio. The rate of change in the salivary cortisol concentrations were significantly higher and that in the T/C ratio was significantly lower in the evening interval training on day 1 in the high-intensity exercise group which had significantly higher running velocity, Borg scale score, and maximum pulse rate values; this relationship was not shown for salivary testosterone.Conclusions: Automated measurements of the salivary cortisol concentration and the T/C ratio reflected different exercise intensities may be useful for creating appropriate exercise programs for athletes. Conversely, the automated measurements of salivary testosterone and T/C ratio, which require passive drooling to collect saliva, may be less suitable for practical use with athletes than the salivary cortisol-only measurement