Stress has been associated with autonomic arousal as well as functional alterations in frontal and limbic regions which are important in the regulation of autonomic activity. Latter can be indexed by heart rate variability (HRV). In the present pilot study simultaneous BOLD fMRI and HRV were measured during the performance of a stress test. In three healthy subjects stress, relaxation and paced breathing were associated with frontal and limbic activation. More subjects need to be measured in order to strengthen the results and to integrate them as neural markers in an integrative and multilevel model of stress.