BACKGROUND: Emotion dysregulation is a core feature of borderline personality disorder (BPD), which often co-occurs with posttraumatic stress disorder (PTSD). Difficulties in emotion regulation (ER) have been linked to lower high-frequency heart rate variability (HF-HRV), a measure of autonomous nervous system functioning. However, previous research on vagally-mediated heart rate in BPD revealed heterogeneous findings and the effects of comorbid PTSD and dissociation on HF-HRV are not yet completely understood. This study aim to investigate HF-HRV during resting-state and an ER task in female BPD patients with comorbid PTSD (BPD + PTSD), patients without this comorbidity (BPD), and healthy controls (HC). METHODS: 57 BPD patients (BPD: n = 37, BPD + PTSD: n = 20) and 27 HC performed an ER task with neutral, positive, and negative images. Participants were instructed to either attend these pictures or to down-regulate their upcoming emotions using cognitive reappraisal. Subjective arousal and wellbeing, self-reported dissociation, and electrocardiogram data were assessed. RESULTS: Independent of ER instruction and picture valence, both patient groups (BPD and BPD + PTSD) reported higher subjective arousal and lower wellbeing; patients with BPD + PTSD further exhibited significantly lower HF-HRV compared with the other groups. Higher self-reported state dissociation predicted higher HF-HRV during down-regulating v. attending negative pictures in BPD + PTSD. CONCLUSIONS: Findings suggest increased emotional reactivity to negative, positive, and neutral pictures, but do not provide evidence for deficits in instructed ER in BPD. Reduced HF-HRV appears to be particularly linked to comorbid PTSD, while dissociation may underlie attempts to increase ER and HF-HRV in BPD patients with this comorbidity.