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Abstract Background Active transportation, such as walking and biking, is a healthy way for children to explore their environment and develop independence. However, children can be injured while walking and biking. Many cities make changes to the built environment (e.g., traffic calming features, separated bike lanes) to keep people safe. There is some research on how effective these changes are in preventing adult pedestrians and bicyclists from getting hurt, but very little research has been done to show how safe various environments are for children and youth. Our research program will study how features of the built environment affect whether children travel (e.g., to school) using active modes, and whether certain features increase or decrease their likelihood of injury. Methods First, we will use a cross-sectional study design to estimate associations between objectively measured built environment and objectively measured active transportation to school among child elementary students. We will examine the associations between objectively measured built environment and child and youth pedestrian-motor vehicle collisions (MVCs) and bicyclist-MVCs. We will also use these data to determine the space-time distribution of pedestrian-MVCs and bicyclist-MVCs. Second, we will use a case-crossover design to compare the built environment characteristics of the site where child and youth bicyclists sustain emergency department reported injuries and two randomly selected sites (control sites) along the bicyclist’s route before the injury occurred. Third, to identify implementation strategies for built environment change at the municipal level to encourage active transportation we will conduct: 1) an environmental scan, 2) key informant interviews, 3) focus groups, and 4) a national survey to identify facilitators and barriers for implementing built environment change in municipalities. Finally, we will develop a built environment implementation toolkit to promote active transportation and prevent child pedestrian and bicyclist injuries. Discussion This program of research will identify the built environment associated with active transportation safety and form an evidence base from which municipalities can draw information to support change. Our team’s national scope will be invaluable in providing information regarding the variability in built environment characteristics and is vital to producing evidence-based recommendations that will increase safe active transportation.