Posttraumatic stress disorder (PTSD) is characterized by psychophysiological abnormalities, such as an altered baseline heart rate and either hyper- or hyporeactivity to a wide range of stimuli, implying dysfunctional arousal regulation. Heart rate variability (HRV) has been established as an important marker of arousal regulatory ability. The aim of the present study was to examine HRV in PTSD under different affective conditions and to explore the role of potential moderating factors. To meet this purpose, videos of varying emotional valence were presented to trauma-exposed participants with PTSD (n = 26), trauma-exposed participants without PTSD (n = 26), as well as non-trauma-exposed controls (n = 18) while HRV was recorded. The PTSD group showed lower HRV than non-trauma-exposed controls at baseline (corrected for age) and throughout different affective conditions implying decreased parasympathetic activity and an inflexible response regulation. There was a negative relationship between HRV and self-report of both depression and state dissociation.