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This paper outlines key experimental design issues associated with the use of psychophysiological measures in human-robot interaction (HRI) studies and summarizes related studies. Psychophysiological measurements are one tool for evaluating participantspsila reactions to a robot with which they are interacting. A brief review of psychophysiology is provided which includes: physiological activities and response tendencies; common psychophysiological measures; and advantages/issues related to psychophysiological measures. Psychophysiological experimental design recommendations are given for information required from participants before the psychophysiological measures are performed; a method to reduce habituation; post-testing assessment process; determining adequate sample sizes; and testing methods commonly used in HRI studies with recommended electrode placements. Psychophysiological measures should be utilized as part of a multi-faceted approach to experimental design including self-assessments, participant interviews, and/or video-recorded data collection methods over the course of an experimental study. Two or more methods of measurement should be utilized for convergent validity. Although psychophysiological measures may not be appropriate for all HRI studies, they can provide a valuable evaluation tool of participantspsila responses when properly incorporated into a multi-faceted experimental design.