Background: Despite strong reservations regarding the validity of a number of heart rate variability (HRV) measures, these are still being used in recent studies. Aims: We aimed to compare the reactivity of ostensible sympathetic HRV markers (low and very low frequency [LF and VLF]) to that of electrodermal activity (EDA), an exclusively sympathetic marker, in response to cognitive and orthostatic stress, investigate the possibility of LF as a vagal-mediated marker of baroreflex modulation, and compare the ability of HRV markers of parasympathetic function (root mean square of successive differences [RMSSD] and high frequency [HF]) to quantify vagal reactivity to cognitive and orthostatic stress. Results: None of the purported sympathetic HRV markers displayed a reactivity that correlated with electrodermal reactivity. LF (ms2) reactivity correlated with the reactivity of both RMSSD and HF during baroreflex modulation. RMSSD and HF indexed the reactivity of the parasympathetic nervous system under conditions of normal breathing; however, RMSSD performed better as a marker of vagal activity when the task required breathing changes. Conclusions: Neither LF (in ms2 or normalized units [nu]) nor VLF represent cardiac sympathetic modulation of the heart. LF (ms2) may reflect vagally mediated baroreflex cardiac effects. HRV linear analysis therefore appears to be restricted to the determination of vagal influences on heart rate. With regard to HRV parasympathetic markers, this study supports the suggestion that HRV frequency domain analyses, such as HF, should not be used as an index of vagal activity in study tasks where verbal responses are required, as these responses may induce respiratory changes great enough to distort HF power.