In the present study we addressed the question of central control of heart rate (HR) in emotions. Parallel measurement of HR changes and changes of local intensity of blood flow as indexed by fMRI in a procedure eliciting emotions allowed us to pinpoint areas of the brain responsible for HR variations during emotional arousal. In condition eliciting positive emotions we detected activation of occipito-temporal regions, anterior insula, and hypothalamus. In condition eliciting negative emotions we also detected activation of occipito-temporal regions and additionally activation of bilateral anterior insulae, right amygdala and right superior temporal gyrus. The results show that structures constituting neural network involved in HR control during emotional arousal are affect specific. Particularly the central circuit controlling HR in negative affect includes the amygdala, while central circuit controlling HR in positive affect includes the hypothalamus. Additionally activation of bilateral occipito-temporal cortex proves enhancement of visual processing of emotional material as compared to neutral material in both positive and negative affect. This might be attributed to top-down processes originating in the frontal lobe and related to shifting attention to the emotionally relevant stimuli. Activation of insular cortex is probably related to autonomic arousal accompanying watching emotional content (e.g. sweating, heart-rate changes etc.). Activation of the amygdala in the negative condition supports the well documented engagement of this structure in processing of fear and disgust.