The goal of our paper is to verify the hypothesis that schools with different educational strategies and school climates, in the context of current diversification of educational system in the Czech Republic, have different impacts on the wellbeing and mental health of children. A sample of 868 schoolchildren from five Prague primary schools was studied. The schools selected for our study represent the spectrum of prevalent educational orientations in transforming compulsory education system. The following indicators of school stress were examined: general anxiety, school anxiety, emotional and psychosomatic balance, learning disabilities and behavioural disorders, type A behaviour, mental capacity, attitudes toward school, and social climate of a class as perceived by pupils. Consequently, selected sample of children underwent a thorough neuropaediatric examination. The findings confirmed our original assumption. The least negative characteristics were found at schools with the climate of confidence and respect among principals, staff, pupils and parents. An authoritarian principal who backs the demanding requirements of the traditional education system may cause a climate of mistrust and fear, anxiety and psychosomatic troubles in the pupils and in teachers as well and learning and behaviour disorders in the pupils. The negative experience endangers healthy development of school population. Thinking about application of our results on health promotion programmes at school, we have concluded that it is of greatest importance to promote changes leading to: confidence between the principal and the staff as well as among teachers themselves, participation and cooperation in school management, conditions for independent and creative work of teachers, teacher's effort to replace directive guidance of pupils by responsibility promoting education, diminishing restrictive role of grading in traditional teaching system and introducing more individual and qualitative evaluation of pupils.