Posttraumatic stress disorder (PTSD) is a prolonged reaction to an extremely traumatic experience. One of the core symptoms of PTSD is hyper-arousal which can be the result of an elevated activation of the autonomic nervous system. Including psychophysiological assessment methods in PTSD research can point to the neurobiological bases of the disorder. The studies of psychophysiology of PTSD to date have mostly measured reactivity. The aim of the current study was to compare resting state psychophysiology and startle reflexes in PTSD patients and controls in a sample of Croatian combat veterans. We measured heart-rate, respiratory sinus arrhythmia, skin conductance, and eyeblink muscle contraction during an acclimation period and during the presentation of startle stimuli in 45 male PTSD patients and 33 male healthy controls. We found that PTSD patient had elevated baseline heart-rate and decreased respiratory sinus arrhythmia compared to the controls. Furthermore, PTSD patients had impaired habituation to the startle probe, but there was no group difference in initial startle magnitude. There was also no group difference in skin conductance level or skin conductance response. Startle habituation and baseline heart-rate appear to offer the most reliable psychophysiological indices of PTSD. This finding replicates trends in the literature in a new population of PTSD patients.