Abstract Background Primarily, this study aims to examine whether children attending sports schools are more active than their counterpart attending normal schools. Secondary, the study aims to examine if physical activity (PA) levels in specific domains differ across school types. Finally, potential modifications by status of overweight/obesity and poor cardio-respiratory fitness are examined. Methods Participants were from the first part of the CHAMPS-study DK, which included approximately 1200 children attending the 0th – 6th grade. At the sports schools, the mandatory physical education (PE) program was increased from 2 to 6 weekly lessons over a 3-year period. Children attending normal schools were offered the standard 2 PE lessons. PA was assessed at two different occasions with the GT3X ActiGraph accelerometer, once during winter in 2009/10 and once during summer/fall in 2010. Leisure time organized sports participation was quantified by SMS track. Based on baseline values in 2008, we generated a high-BMI and a low-cardio-respiratory fitness for age and sex group variable. Results There were no significant differences in PA levels during total time, PE, or recess between children attending sports schools and normal schools, respectively. However, children, especially boys, attending sports schools were more active during school time than children attending normal schools (girls: β=51, p=0.065; boys: β=113, p