Obesity during adolescence has multi-system health consequences. The objective of this work was to determine whether pre-adolescent overweight/obese children's bones respond to a 9-month physical activity intervention by increasing bone density similar to healthy-weight children.Participants included overweight/obese (BMI >85%) and healthy weight (15% < BMI <85%) preadolescents (8-9years old). Participants in the physical activity group participated in a 9-month physical activity curriculum every day after school. The wait-list control group received no intervention. Both groups had overweight/obese children and healthy-weight controls. Whole body bone mineral content (BMC), area, and bone mineral apparent density (BMAD) were assessed using dual X-ray absorptiometry) at the beginning and end of the 9-month trial in the physical activity and control group.Overweight/obese pre-adolescent children had higher BMAD than healthy weight children (p<0.001 for spine, leg, and whole body). However, the density/weight (BMAD/lean mass) was lower in overweight/obese children than in healthy weight children indicating the density of bones in overweight/obese children may not compensate sufficiently for the excessive load due to weight. The change in BMAD over 9 months was greater in healthy weight children than overweight/obese children in the whole body and leg, but not the lumbar spine. Physical activity caused a site-specific increase in bone density, affecting the legs more than the lumbar spine, but there was no significant difference in the effect of exercise between the healthy weight and overweight/obese group.The smaller change in BMAD over the 9 months and lower BMAD per unit lean mass in overweight/obese compared to healthy weight children may indicate a slower rate of bone mass accrual, which may have implications for bone health during skeletal growth in obese/overweight children.