Obesity treatment is by large ineffective long term, and more emphasis on the prevention of excessive weight gain in childhood and adolescence is warranted. To inform energy balance related behaviour (EBRB) change interventions, insight in the potential personal, family and school environmental correlates of these behaviours is needed. Studies on such multilevel correlates of EBRB among schoolchildren in Europe are lacking. The ENERGY survey aims to (1) provide up-to-date prevalence rates of measured overweight, obesity, self-reported engagement in EBRBs, and objective accelerometer-based assessment of physical activity and sedentary behaviour and blood-sample biomarkers of metabolic function in countries in different regions of Europe, (2) to identify personal, family and school environmental correlates of these EBRBs. This paper describes the design, methodology and protocol of the survey.