Measurement of physical fitness and physical activity in children and adolescents raise a lot of methodological issues, explaining the scarcity of surveys in European countries and in Switzerland. This article exposes the design and the methods used in a survey on physical fitness, physical activity and health conducted in a region of Switzerland, and discuss the choice of the instruments and the quality control procedure selected to measure physical activity and physical fitness. The survey was conducted in a sample of 3540 students 9-19 years-old and included a battery of physical fitness tests, anthropometrics measurements and a self-report questionnaire on physical activity, sports activity and life styles. An ancillary study in a sub sample assessed daily physical activity with a pedometer, dietary intake with a 3-day dietary record, serum lipids and nutritional status. Some results are displayed as example. Quality control techniques are exposed and the choice of the instrument to assess physical fitness, physical activity, sports, and dietary intake are discussed. Local reference tables are now available for fitness tests and the practicability of fitness testing has been demonstrated in physical education. The research process has induced the sensitisation of schools toward health promotion through physical activity.