<b><i>Introduction:</i></b> Given the growing evidence of reduced heart rate variability in psychiatric diseases associated with emotional instability, we investigated cardiovascular autonomic modulation in patients with borderline personality disorder (BPD) during resting state, parasympathetic stimulation (metronomic breathing), and sympathetic stimulation (mental arithmetic stress test). <b><i>Methods:</i></b> In 29 BPD outpatients and 30 controls, we recorded RR-intervals (RRI), blood pressure, skin conductance levels, and respiratory frequency during resting state, metronomic breathing, stress anticipation, stress exposure, and stress recovery. We calculated baroreflex sensitivity (BRS) and parameters of heart rate variability, including the root mean square of successive differences (RMSSD), an index of cardiovagal modulation. <b><i>Results:</i></b> During resting state, BPD patients showed higher blood pressure and shorter RRI, as well as lower RMSSD and BRS than controls. Metronomic breathing increased RMSSD and BRS in BPD patients. During the stress exposure, BRS significantly decreased in controls, but not in BPD patients. Furthermore, BPD patients showed less cardioacceleration in response to stress exposure than controls. During stress recovery, we found increases in RMSSD and BRS in controls, but not in BPD patients. <b><i>Conclusion:</i></b> Our data show reduced cardiovascular autonomic modulation in BPD patients during resting state, psychophysiological relaxation, and stress exposure. The results indicate a vagal modulation deficit in this cohort. Breathing techniques, such as metronomic breathing, might be helpful to reduce stress and to increase vagal tone in BPD patients.