This protocol offers a detailed description of a psychophysiological experiment using script-driven trauma-related imagery and standardized clinical instruments within a comparative design assessing physiological and psychopathological features of individuals with BPD. This method aims at studying the psychological and physiological effects of trauma-related dissociation. Since the psychodiagnostic classification of trauma-related disorders relies on the observation of evolutionarily determined responses to life-threat, an integrated assessment paradigm for the study of reactions to traumatic memories proposes a very appropriate methodological approach. The employed script-driven imagery paradigm uses individual recall instructions to activate trauma-related memory networks and prompt associated emotional and physiological responses. These responses are measured by means of self-rating scales and physiological assessments. During the individual recall, participants are asked to vividly imagine traumatic and everyday experiences and other situations triggered by short personalized verbal scripts they authored beforehand together with the experimenters. A wide range of affective reactions and different physiological parameters can be measured. We used this paradigm to investigate dissociative states in BPD and to find physiological and affective correlates of dissociative states. Some of the participants were having severe traumatic antecedents. To investigate different reaction patterns within the same diagnostic group, participants with different levels of traumatic histories, symptom severities, and co-morbidities should be included. By using short verbal scripts, the level of stress induced to participants is held as low as possible without affecting the validity of the object of investigation.