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Psychological discomfort and stress may negatively affect various work activities especially in professions that are directly responsible for the lives and health of human beings. We can find these kinds of professions mainly in civil aviation, specifically the profession of a pilot. Analysis showed, that the legislative requirements for the qualifications of a pilot, require only the competence for a particular aircraft but they don't take in account the ergonomics of the cabin and the visualization of the basic flight data (analog, glass-cockpit). That's the reason why this paper assesses the influence of flight, navigation and engine data visualization on psychophysiological state of the pilot. In this paper we used the measuring of the heart rate as the main indicator of stress. Spectral analysis was used for the assessment of stress levels with main focus on the activity of the autonomic nervous system. The evaluation was based on twenty subjects in flight training, which were divided into two groups. Each group had different methods of training based on flight data visualization. The results show that the group with the more extensive glass-cockpit training exhibit lower values of psychophysiological stress. These findings may contribute to the increase of aviation safety and the description of human-machine interface in aviation.