A characteristic notch in the heart rate (fc) on-response at the beginning of square-wave exercise is described in 7 very fit marathon runners and 12 sedentary young men, during cycle tests at 30% and 60% of maximal oxygen consumption (VO2max). The fc notch revealed a fc overshoot with respect to the fc values predicted from exponential beat-by-beat fitted models. While at 30% of VO2max all subjects showed a fc overshoot, at 60% of VO2max it occurred in the marathon runners but not in the sedentary subjects. The mean time of occurrence of the fc overshoot from the onset of the exercise was 16.7 (SD 4.7) s and 12.2 (SD 3.2) s at 30% of VO2max in the runners and the sedentary subjects respectively, and 23.8 (SD 8.8) s at 60% of VO2max in the runners. The amplitude of the overshoot, with respect to rest, was 41 (SD 12) beats.min-1 and 31 (SD 4) beats.min-1 at 30% of VO2max in the runners and the sedentary subjects respectively, and 46 (SD 19) beats.min-1 at 60% of VO2max in the runners. The existence and the amplitude of the fc overshoot may have been related to central command and muscle heart reflex mechanisms and thus may have been indicators of changes in the balance between sympathetic and parasympathetic activity occurring in fit and unfit subjects.