Abstract Background Physical activity and sedentary behaviour among children should be measured accurately in order to investigate their relationship with health. Accelerometry provides objective and accurate measurement of body movement, which can be converted to meaningful behavioural outcomes. The aim of this study was to evaluate the best evidence for the decisions on data collection and data processing with accelerometers among children resulting in a standardized protocol for use in the participating countries. Methods/Design This cross-sectional accelerometer study was conducted as part of the European ENERGY-project that aimed to produce an obesity prevention intervention among schoolchildren. Five countries, namely Belgium, Greece, Hungary, Switzerland and the Netherlands participated in the accelerometer study. We used three different Actigraph models-Actitrainers (triaxial), GT3Xs and GT1Ms. Children wore the device for six consecutive days including two weekend days. We selected an epoch length of 15 seconds. Accelerometers were placed at children's waist at the right side of the body in an elastic belt. In total, 1082 children participated in the study (mean age = 11.7 ± 0.75 y, 51% girls). Non-wearing time was calculated as periods of more than 20 minutes of consecutive zero counts. The minimum daily wearing time was set to 10 hours for weekdays and 8 hours for weekend days. The inclusion criterion for further analysis was having at least three valid weekdays and one valid weekend day. We selected a cut-point (count per minute (cpm)) of 5200 cpm for vigorous physical activity. We also created time filters for school-time during data cleaning in order to explore school-time physical activity and sedentary behaviour patterns in particular. Discussion This paper describes the decisions for data collection and processing. Use of standardized protocols would ease future use of accelerometry and the comparability of results between studies.