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This review paper is concerned with the development of physiological computing systems that employ real-time measures of psychophysiology to communicate the psychological state of the user to an adaptive system. It is argued that physiological computing has enormous potential to innovate human-computer interaction by extending the communication bandwidth to enable the development of 'smart' technology. This paper focuses on six fundamental issues for physiological computing systems through a review and synthesis of existing literature, these are (1) the complexity of the psychophysiological inference, (2) validating the psychophysiological inference, (3) representing the psychological state of the user, (4) designing explicit and implicit system interventions, (5) defining the biocybernetic loop that controls system adaptation, and (6) ethical implications. The paper concludes that physiological computing provides opportunities to innovate HCI but complex methodological/conceptual issues must be fully tackled during the research and development phase if this nascent technology is to achieve its potential.