Background: The aim of this 12-month study in pre-pubertal children was to evaluate the effect of school transportation on gain in lean and fat mass, muscle strength and physical performance. Methods: Ninety-seven girls and 133 boys aged 7-9 years from the Malmö Pediatric Osteoporosis Prevention Study were included. Regional lean and fat mass were assessed by dual energy X-ray absorptiometry, isokinetic peak torque of knee extensors and flexors by a computerised dynamometer and physical performance by vertical jump height. Level of physical activity was assessed by accelerometers. The 12-month changes in children who walked or cycled to school were compared with changes in those who travelled by bus or car. Results: There were no differences in baseline or annual changes in lean or fat mass gain, muscle strength or physical performance between the two groups. All children reached the internationally recommended level of 60 minutes per day of moderate or high physical activity by accelerometers. Conclusion: The choice of school transportation in pre-pubertal children seems not to influence the gain in lean and fat mass, muscle strength or functional ability, probably as the everyday physical activity is so high that the mode of school transportation contributes little to the total level of activity.