The risk of adverse cardiovascular events is elevated in the morning compared to the rest of the day. A circadian and a sleep-wake dependent variation in the regulation of the cardiovascular system could contribute to this increased cardiovascular risk. Using an ultradian sleep-wake cycle (USW) procedure, our aim was to explore the effects of the sleep-wake and circadian cycles on cardiorespiratory coherence (CRC) as a measure of autonomic nervous system (ANS) state. Our results suggest a shift toward parasympathetic dominance with deepening of sleep. Conversely, REM sleep is associated with a sympathetic dominance comparable to levels observed during wakefulness. A circadian rhythm was observed for CRC during wakefulness and all sleep stages. Maximal sympathetic dominance was observed in the morning, as measured by CRC during wakefulness and REM sleep, consistent with studies showing increased cardiac risk in the morning. This study provides evidence that circadian and sleep processes interact to influence the ANS modulation of the heart.