--- - |2 Abstract Our environment is constantly overloaded with information, although we cannot consciously process all the stimulation reaching our senses. Current theoretical models are focused on the cognitive and neural processes underlying conscious perception. However, cognitive processes do not occur in an isolated brain but in a complex interaction between the environment, the brain, and the organism. The brain‐body interaction has largely been neglected in the study of conscious perception. The aim of the present study was to explore if heart rate and skin conductance (SC) are modulated by the interaction between phasic alertness and conscious perception. We presented near‐threshold visual stimuli that could be preceded by an alerting tone on 50% of the trials. Behaviorally, phasic alerting improved perceptual sensitivity for detecting a near‐threshold stimulus (along with changes in response criterion). Following the alerting tone, a cardiac deceleration‐acceleration pattern was observed, which was more pronounced when the near‐threshold stimulus was consciously perceived in comparison with unconsciously perceived stimuli. SC results further showed some degree of subliminal processing of unseen stimuli. These results reveal that cardiac activity could be a marker of attention and consciousness interactions, emphasizing the need for taking into account brain‐body interactions for current theoretical models of consciousness. - Psychophysiology, EarlyView.