AbstractMaintaining temporal coordination across physiological systems is crucial at the wake-sleep transition. As shown in recent studies, the degree of coordination between brain and autonomic arousal influences attention, which highlights a previously unrecognised point of potential failure in the attention system. To investigate how cortical and autonomic dynamics are linked to the attentive process we analysed electroencephalogram, electrocardiogram and skin conductance data of 39 healthy adults recorded during a 2-h resting-state oddball experiment. We related cross-correlations to fluctuation periods of cortical and autonomic signals and correlated obtained measures to event-related potentials N1 and P2, reflecting excitatory and inhibitory processes. Increasing alignment of cortical and autonomic signals and longer periods of vigilance fluctuations corresponded to a larger and earlier P2; no such relations were found for N1. We compared two groups, with (I) and without measurable (II) delay in cortico-autonomic correlations. Individuals in Group II had more stable vigilance fluctuations, larger and earlier P2 and fell asleep more frequently than individuals in Group I. Our results support the hypothesis of a link between cortico-autonomic coupling and dynamics and central inhibition. Quantifying this link could help refine classification in psychiatric disorders with attention and sleep-related symptoms, particularly in ADHD, depression, and insomnia.