The frequency of adverse cardiovascular events is greater in the morning compared to its 24-hour average. A circadian variation in the regulation of the cardiovascular system could contribute to this increased cardiovascular risk in the morning. Indeed, circadian rhythms have been shown for a wide array of physiological processes. Using an ultradian sleep-wake cycle (USW) procedure, we sought to determine how heart rate (HR) and heart rate variability (HRV) correlate with the well-characterized circadian rhythms of cortisol and melatonin secretion. Specific HRV components, namely the low frequency (LF) power, high frequency (HF) power, and the LF:HF ratio can be used as markers of the autonomic modulation of the heart. Cross-correlation between HRV parameters and hormonal rhythms demonstrated that mean RR interval is significantly phase-advanced relative to salivary cortisol and urinary 6-sulfatoxy-melatonin (UaMt6s). Parasympathetic modulation of the heart (HF power) was phase-advanced relative to cortisol, but was in-phase with UaMt6s levels. Maximal correlation of the sympathovagal balance (the LF:HF ratio) had no significant lag compared to cortisol secretion and UaMt6s excretion. The protective effect of the parasympathetic nervous system at night, combined with the putative risk associated with the sympathetic nervous system peaking in the morning, could be associated with the increased cardiovascular risk observed in the morning hours.