The sustainability of the development of society depends and is secure by the safety of health of human capital. The article presents the results of a study of gender differences in adaptive reactions of students in the development of educational innovations using the non-invasive method of heart rate variability. Comparative analysis of heart rate measurements among the surveyed students showed that both boys and girls had tachycardia during the lessons. In boys, an increase in the stress index revealed that was reliably associated with the tension of the parasympathetic system, and in girls - the sympathetic system of autonomic regulation of heart rhythm control. A wide individual range of adaptive reactions of the cardiovascular system of young men and women to the impact of ICT revealed. The data obtained more indicative of biological (sex) differences in adaptive responses in the implementation of information technology in education. Our research has shown gender differences in adaptive responses. We observed a significant correlation between stress and the reaction of the autonomic nervous system. It is necessary to prevent the disturbance of the adaptive of the body. Therefore, we must create a safe environment for the health of students. It is desirable to reduce the time spent in the information space (up to 80 minutes, followed by a break). Since the research conducted on a small sample and one educational institution, it is necessary to research this issue on a larger representative sample.