The purpose of this study was to verify the heart rate variability (HRV) and heart rate (HR) kinetics during the fundamental phase in different intensity domains of cycling exercise. Fourteen males performed five exercise sessions: (1) maximal incremental cycling test; (2) two rest-to-exercise transitions for each intensity domain, that is, heavy (Delta30) and severe (Delta60) domains. HRV markers (SD1 and SD2) and HR kinetics in the fundamental phase were analyzed by first-order exponential fitting. There were no significant differences in amplitude values between SD1(Delta30) (8.98 +/- 3.52 ms) and SD1(Delta60) (9.44 +/- 3.24 ms) and SD2(Delta30) (24.93 +/- 9.16 ms) and SD2(Delta60) (25.98 +/- 7.29 ms). Significant difference was observed between HR(Delta30) (52 +/- 7 bpm) and HR(Delta60) (63 +/- 8 bpm). The time constant (tau) values were significantly different between SD1(Delta30) (17.61 +/- 6.26 s) and SD1(Delta60) (13.86 +/- 5.90 s), but not between SD2(Delta30) (20.06 +/- 3.73 s) and SD2(Delta60) (19.47 +/- 6.03 s) or HR(Delta30) (56.75 +/- 18.22 s) and HR(Delta60) (58.49 +/- 15.61 s). However, the tau values for HR(Delta30) were higher and significantly different in relation to SD1(Delta30) and SD2(Delta30), as well as for HR(Delta60) in relation to SD1(Delta60) and SD2(Delta60). The kinetics of the autonomic variable (SD1 marker) was accelerated by the increased intensity. Moreover, significant differences were found for the tau values, with faster HRV markers than HR, in both intensities of Delta30 and Delta60, which suggests that these variables indicate distinct and specific cardiac autonomic response times during different intensity domains in cycling.HIGHLIGHTSThe application of HRV to optimize exercise prescription at different effort intensities is extremely important to obtain assertive and effective results.Analysis of the kinetic responses of HRV is a useful tool for the evaluation of exercise performance and health status.A faster kinetics was found for HRV markers in comparison to HR, for both intensities analysed, which suggests that these variables indicate distinct and specific cardiac autonomic response times during different intensity domains in cycling.