The analysis and interpretation of heart rate variability (HRV) during exercise is challenging not only because of the non-stationary nature of exercise, the time-varying mean heart rate and the fact that respiratory frequency exceeds 0.4 Hz. There are also other factors, such as the component centred at the pedalling frequency observed in maximal cycling tests, which may confuse the interpretation of HRV analysis. The objectives of this study are to test the hypothesis that a component centred at the running stride frequency appears in the HRV of subjects during maximal treadmill exercise testing, and to study its influence in the interpretation of the low frequency (LF) and high frequency (HF) components of HRV during exercise. The HRV of 23 subjects during maximal treadmill exercise testing is analyzed. The instantaneous power of different HRV components is computed from the smoothed pseudo Wigner-Ville distribution of the modulating signal assumed to carry information from the autonomic nervous system, which is estimated based on the time-varying integral pulse frequency modulation model. Besides the LF and HF components, the appearance is revealed of a component centred at the running stride frequency as well as its aliases. The power associated with the stride frequency component and its aliases represents 22±7% (median±median absolute deviation) of the total HRV power in all the subjects. Normalized LF power decreases as the exercise intensity increases, while normalized HF power increases. The power associated with the stride frequency does not change significantly with exercise intensity. Consideration of the running stride frequency component and its aliases is very important in HRV analysis since stride frequency aliases may overlap with LF and HF components.