Traditional educational organizations to preserve the health of pupils is to establish judicial educational environment. The work focuses on the development of personal qualities of students, formation of their preparedness for health. This corresponds to the core activities of educational organizations (training, education and development) and to review how the target focus on preservation of health of pupils and measures of its effectiveness. The system of integrated assessment modelling activities to preserve the health of pupils, which follows the structure of the components of the quality of education: the quality of the environment, the quality of the processes and the quality of the results of students ' health. The use of the proposed comprehensive system of assessment is an important tool in quality management of educational organizations to safeguard the health of pupils. Shows the results of experimental work confirming the effectiveness of educational organizations to safeguard the health of pupils depends on completeness of implementation of appropriate conditions to ensure its quality.