Background Migraine is a stress-related disorder, suggesting that there may be sympathetic hyperactivity in migraine patients. However, there are contradictory results concerning general sympathetic activation in migraine patients. To shed more light on the involvement of the autonomic nervous system (ANS) in migraine pathophysiology, we investigated cardiac and cardiovascular reactions during vagal (paced breathing) and sympathetic activation (mental stress test). Methods Heart rate variability parameters and skin conductance responses were recorded interictally in 22 episodic migraine patients without aura and 25 matched controls during two different test conditions. The paced breathing test consisted of a five-minute baseline, followed by two minutes of paced breathing (6 breathing cycles per minute) and a five-minute recovery phase. The mental stress test consisted of a five-minute baseline, followed by one minute of stress anticipation, three and a half minutes of mental stress and a five-minute recovery phase. Furthermore we measured blood pressure and heart rate once daily over 2 weeks. Subjects rated their individual current stress level and their stress level during paced breathing and during the mental stress test. Results There were no significant differences between migraine patients and controls in any of the heart rate variability parameters in either time domain or frequency domain analysis. However, all parameters showed a non-significant tendency for larger sympathetic activation in migraine patients. Also, no significant differences could be observed in skin conductance responses and average blood pressure. Only heart rates during the 2-week period and stress ratings showed significantly higher values in migraine patients compared to controls. Conclusions Generally there were no significant differences between migraine patients and controls concerning the measured autonomic parameters. There was a slight but not significant tendency in the migraine patients to react with less vagal and more sympathetic activation in all these tests, indicating a slightly changed set point of the autonomic system. Heart rate variability and blood pressure in migraine patients should be investigated for longer periods and during more demanding sympathetic activation.