Electrodermal activity reflects autonomic sympathetic innervation of dermal sweat glands providing an index of emotion-related bodily states of arousal. Relaxation techniques, which are facilitated by external (bio)feedback of electrodermal activity, can be used by trained subjects to actively control bodily and emotional arousal. Biofeedback relaxation provides an experimental model to explore neural mechanisms contributing to emotional representations and intentional autonomic control. We used functional magnetic resonance imaging (fMRI) to explore neural mechanisms contributing to integration of volitional intent, self-representation, and autonomic states of arousal, embodied within performance of a biofeedback relaxation exercise. Data were obtained from 17 subjects to assess brain activity during relaxation in which a visual index of electrodermal arousal was modulated by accuracy (addition of random "noise") or sensitivity (by scalar adjustments of feedback). A central matrix of cortical, subcortical and brainstem autonomic centres was activated during biofeedback relaxation, as well as regions that mediate visual and somatesthetic representations and executive control. Anterior cingulate, amygdala, and insula activity was modulated by task manipulations that increased demand on processing interoceptive representations, while variation in anterior insula activity reflected an interaction between accuracy and sensitivity of feedback. These findings identify neural substrates that support integration of perceptual processing, interoception, and intentional modulation of bodily states of arousal.