The human brain can encode auditory regularities with fixed sound-to-sound intervals and with sound onsets locked to cardiac inputs. Here, we investigated auditory and cardio-audio regularity encoding during sleep, when bodily and environmental stimulus processing may be altered. Using electroencephalography and electrocardiography in healthy volunteers (N = 26) during wakefulness and sleep, we measured the response to unexpected sound omissions within three regularity conditions: synchronous, where sound and heartbeat are temporally coupled, isochronous, with fixed sound-to-sound intervals, and a control condition without regularity. Cardio-audio regularity encoding manifested as a heartbeat deceleration upon omissions across vigilance states. The synchronous and isochronous sequences induced a modulation of the omission-evoked neural response in wakefulness and N2 sleep, the former accompanied by background oscillatory activity reorganization. The violation of cardio-audio and auditory regularity elicits cardiac and neural responses across vigilance states, laying the ground for similar investigations in altered consciousness states such as coma and anaesthesia.