The variability of heart period, measured as the time distance between two consecutive QRS complexes from the electrocardiogram (RR), was exploited to infer cardiac vagal control, while the variability of the duration of the electrical activity of the heart, measured as the time interval from Q-wave onset to T-wave end (QT), was proposed as an indirect index of cardiac sympathetic modulation. This study tests the utility of the concomitant evaluation of RR variability (RRV) and QT variability (QTV) markers in typifying cardiac autonomic control of humans under different experimental conditions and of rat groups featuring documented differences in resting sympatho-vagal balance. We considered: (i) 23 healthy young subjects in resting supine position (REST) undergoing head-up tilt at 45° (T45) and 90° (T90) followed by recovery to the supine position; (ii) 9 Wistar (WI) and 14 wild-type Groningen (WT) rats in unstressed conditions, where the WT animals were classified as non-aggressive (non-AGG, n = 9) and aggressive (AGG, n = 5) according to the resident intruder test. In humans, spectral analysis of RRV and QTV was performed over a single stationary sequence of 250 consecutive values. In rats, spectral analysis was iterated over 10-min recordings with a frame length of 250 beats with 80% overlap and the median of the distribution of the spectral markers was extracted. Over RRV and QTV we computed the power in the low frequency (LF, from 0.04 to 0.15 Hz in humans and from 0.2 to 0.75 Hz in rats) band (LFRR and LFQT) and the power in the high frequency (HF, from 0.15 to 0.5 Hz in humans and from 0.75 to 2.5 Hz in rats) band (HFRR and HFQT). In humans the HFRR power was lower during T90 and higher during recovery compared to REST, while the LFQT power was higher during T90. In rats the HFRR power was lower in WT rats compared to WI rats and the LFQT power was higher in AGG than in non-AGG animals. We concluded that RRV and QTV provide complementary information in describing the functioning of vagal and sympathetic limbs of the autonomic nervous system in humans and rats.