There is a continuing debate concerning "adjustments" to heart period variability [i.e., heart rate variability (HRV)] for the heart period [i.e., increases inter-beat-intervals (IBI)]. To date, such arguments have not seriously considered the impact a demographic variable, such as gender, can have on the association between HRV and the heart period. A prior meta-analysis showed women to have greater HRV compared to men despite having shorter IBI and higher heart rate (HR). Thus, it is plausible that men and women differ in the association between HRV and HR/IBI. Thus, the present study investigates the potential moderating effect of gender on the association between HRV and indices of cardiac chronotropy, including both HR and IBI. Data from 633 participants (339 women) were available for analysis. Cardiac measures were assessed during a 5-min baseline-resting period. HRV measures included the standard deviation of inter-beat-intervals, root mean square of successive differences, and autoregressive high frequency power. Moderation analyses showed gender significantly moderated the association between all HRV variables and both HR and IBI (each p < 0.05). However, results were not consistent when using recently recommended HRV variables "adjusted" for IBI. Overall, the current investigation provides data illustrating a differential association between HRV and the heart period based on gender. Substantial neurophysiological evidence support the current findings; women show greater sensitivity to acetylcholine compared to men. If women show greater sensitivity to acetylcholine, and acetylcholine increases HRV and the heart period, then the association between HRV and the heart period indeed should be stronger in women compared to men. Taken together, these data suggest that routine "adjustments" to HRV for the heart period are unjustified and problematic at best. As it relates to the application of future HRV research, it is imperative that researchers continue to consider the potential impact of gender.