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The importance of the bi-directional communication between the heart and brain has been known for over 100 years (Lane et al. in NeuroImage 44:213–222, 2009a, Psychosom Med 2:117–134, 2009b) and plays an important role in many of the prominent theories of psychophysiology today. Utilizing heartbeat evoked potentials (HEPs), we sought to determine whether heart rate variability (HRV) was related to the strength of the connection between the heart and brain. We also hypothesized that differing emotion states would result in differing amplitudes of HEPs. Participants were induced into emotional states with an autobiographical script of their happiest and saddest memory. HEPs were also recorded during diaphragmatic breathing at six breaths per minute. The evoked potentials during the emotional conditions, especially negative emotion were most attenuated. We believe that the signal from the heart to the brain may be filtered by central limbic structures affecting the level of the signal at the cortex. It also appears that HRV affects the strength of HEPs, especially during resonant breathing. Significant neurocardiac gender differences were also present across all conditions. The results of this study support the theory and speculation of many authors who believe vagal afferents play a role in brain function.