A number of studies have demonstrated that patients suffering from PTSD show differences from appropriate controls in psychophysiological responding. This study aimed to investigate whether there were differences in habituation and psychophysiological reactivity between PTSD patients and normals, and between patient subgroups depending on their symptoms and whether psychophysiological variables were associated with clinical outcome from a treatment trial. Participants were tested by measuring electrodermal activity to two sets of 15 auditory stimuli of different intensity, and to six vignettes, four neutral, one of general stress and one trauma related. Psychophysiological variables were entered into a multiple regression with clinical outcome as the dependent variable. There were no differences between patients and controls or within patients on the habituation paradigms. Patients differed from controls only on their response to the trauma related vignette. There were no differences on any within patient comparisons. There was no association with these measures and later clinical outcome. Psychophysiological differences between PTSD patients and normal controls are very specifically related to trauma related stimuli. Patients with startle or high arousal symptoms do not show differences from those without. These measures were not related to treatment response.