To explore whether depth of sleep is related to changes in autonomic control in rats, continuous power-spectral analysis of electroencephalogram (EEG) and heart rate variability (HRV) was performed in unanesthetized rats during normal daytime sleep. Quiet sleep (QS) was associated with an increase in high-frequency power of HRV (0.6-2.4 Hz, HF) but a decrease in low-frequency power (0.06-0.6 Hz) to HF ratio (LF/HF) compared with awakening. During QS, LF/HF was significantly and negatively correlated with delta power of EEG (0.5-4.0 Hz), whereas mean R-R interval and HF were not. As in humans, cardiac sympathetic regulation in rats is negatively related to the depth of sleep during QS, although vagal regulation is not. Our methodology offers a parallel way of studying the interaction between cerebral cortical and autonomic functions in rats.