BACKGROUND: We hypothesize that the population with borderline personality shows different autonomic response to methadone compared to individuals with other personalities. This study applies heart rate variability (HRV) measurements and the Tridimensional Personality Questionnaire (TPQ) to examine this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Forty-four male patients with heroin dependence were recruited from a methadone maintenance treatment program. Eight personality patterns were classified according to the TPQ norm used in Taiwan. The borderline pattern (BP, composed of high novelty seeking, high harm avoidance and low reward dependence) and the other personality patterns (OP) were separated into two groups. We compared the HRV profiles between the BP and OP groups. Correlation and regression analysis were performed to clarify relationship between HRV differences and the borderline index (BI, a new concept defined by us, which is calculated as novelty seeking + harm avoidance - reward dependence). The HRV targets investigated included low frequency (LF) power, high frequency (HF) power, total power (TP), normalized LF (LF%), and LF/HF. No baseline HRV parameters showed any inter-group difference. The BP group had a significantly lower DeltaHF and a higher DeltaLF/HF than the OP group. The personality dimension, reward dependence, showed a negative correlation with DeltaLF/HF and DeltaLF%. BI was negatively correlated with DeltaHF and positively correlated with DeltaLF/HF and DeltaLF%. CONCLUSIONS/SIGNIFICANCE: Borderline personality individuals show increased sympathetic activity and decreased parasympathetic activity compared to other personalities after taking methadone. The results support the hypothesis that there is an interaction between borderline personality and autonomic modulation.