Objective: To determine the independent contributions of family and neighbourhood environments to changes in youth physical activity and body mass index (BMI) z-score over 5 years. Methods: In 2001 years at baseline) had their height and weight measured (BMI was converted to z-scores using Centers for Disease Control and Prevention reference charts; see http://www.cdc.gov/growthcharts) and moderate-to-vigorous physical activity (MVPA) assessed using accelerometers. In 2001, parents reported on the home environment (social support, role modelling, rules and restrictions, physical environment) and perceived neighbourhood environment (local traffic, road safety, sporting venues, public transport), and Geographic Information Systems were used to map features of the neighbourhood environment (destinations, road connectivity, traffic exposure). Generalized estimating equations were used to predict average BMI z-score and MVPA over time from baseline home and perceived and objective neighbourhood environment factors. Results: Among boys, maternal education and heavy traffic were inversely associated, and sibling physical activity, maternal role modelling of MVPA and the presence of dead-end roads were positively associated with MVPA. Having unmarried parents, maternal MVPA role modelling and number of home sedentary items were positively associated with BMI z-score among boys. Among girls, having siblings, paternal MVPA role modelling, physical activity rules and parental physical activity co-participation were positively associated with MVPA. Having unmarried parents and maternal sedentary behaviour role modelling were positively associated, and number of sedentary behaviour rules and physical activity items were inversely associated with BMI z-score among girls. Conclusion: The home environment seems more important than the neighbourhood environment in influencing children's physical activity and BMI z-score over 5 years. Physical activity and weight gain programmes among youth should focus on parental role modelling, rules around sedentary and active pursuits, and parental support for physical activity. Intervention studies to investigate these strategies are warranted.