Objective: To test whether ventilatory thresholds, measured during an exercise test, could be assessed using time varying analysis of respiratory sinus arrhythmia frequency (f(RSA)). Methods: Fourteen sedentary subjects and 12 endurance athletes performed a graded and maximal exercise test on a cycle ergometer: initial load 75 W (sedentary subjects) and 150 W (athletes), increments 37.5 W/2 min. f(RSA) was extracted from heart period series using an evolutive model. First (T-V1) and second (T-V2) ventilatory thresholds were determined from the time course curves of ventilation and ventilatory equivalents for O-2 and CO2. Results: f(RSA) was accurately extracted from all recordings and positively correlated to respiratory frequency (r = 0.96 (0.03), p < 0.01). In 21 of the 26 subjects, two successive non-linear increases were determined in f(RSA), defining the first (T-RSA1) and second (T-RSA2) f(RSA) thresholds. When expressed as a function of power, T-RSA1 and T-RSA2 were not significantly different from and closely linked to T-V1 (r = 0.99, p < 0.001) and T-V2 (r = 0.99, p < 0.001), respectively. In the five remaining subjects, only one non-linear increase was observed close to T-V2. Significant differences (p < 0.04) were found between athlete and sedentary groups when T-RSA1 and T-RSA2 were expressed in terms of absolute and relative power and percentage of maximal aerobic power. In the sedentary group, T-RSA1 and T-RSA2 were 150.3 (18.7) Wand 198.3 (28.8) W, respectively, whereas in the athlete group T-RSA1 and T-RSA2 were 247.3 (32.8) W and 316.0 (28.8) W, respectively. Conclusions: Dynamic analysis of f(RSA) provides a useful tool for identifying ventilatory thresholds during graded and maximal exercise test in sedentary subjects and athletes.