Background: Cycling to and from school is an important source of physical activity (PA) in youth but it is not captured by the dominant objective method to quantify PA. The aim of this study was to quantify the underestimation of objectively assessed PA caused by cycling when using accelerometry. Methods: Participants were 20 children aged 11-14 years from a randomized controlled trial performed in 2011. Physical activity was assessed by accelerometry with the addition of heart rate monitoring during cycling to school. Global positioning system (GPS) was used to identify periods of cycling to school. Results: Mean (95% CI) minutes of moderate-to-vigorous physical activity (MVPA) during round-trip commutes was 10.8 (7.1 - 16.6). Each kilometre of cycling meant an underestimation of 9314 (95%CI: 7719 - 11238) counts and 2.7 (95%CI: 2.1 - 3.5) minutes of MVPA. Adjusting for cycling to school increased estimates of MVPA/day by 6.0 (95%CI: 3.8 - 9.6) minutes. Conclusions: Cycling to and from school contribute substantially to levels of MVPA and to mean counts/min in children. This was not collected by accelerometers. Using distance to school in conjunction with self-reported cycling to school may be a simple tool to improve the methodology.