We investigated differences in physical activity (PA) levels between black and white South African 9 year olds and their association with bone mineral content (BMC) and density (BMD) using dual-energy X-Ray absorptiometry (DXA). PA was analyzed in terms of a metabolic (METPA; weighted metabolic score of intensity, frequency and duration) and a mechanical (MECHPA; sum of all ground reaction forces multiplied by duration) component. There were significant ethnic differences in patterns of activity. White children expended a significantly greater energy score (METPA 21.7 ± 2.9) than black children (9.5 ± 0.5) (p<0.001). When children were divided into quartiles according to the amount and intensity of sport played, the most active white children (using METPA scores) had significantly higher whole body BMD, and hip and spine BMC and BMD than less active children. White children in the highest MECHPA quartile also showed significantly higher whole body, hip and spine BMC and BMD than those children in the lowest quartile. No association between exercise and bone mass of black children was found. In this population, PA has an osteogenic association with white children, but not black children, which may be explained by the lower levels of PA in the black children. Despite this, black children had significantly greater bone mass at the hip and spine (girls only) (p<0.001) even after adjustment for body size. The role of exercise in increasing bone mass may become increasingly critical as a protective mechanism against osteoporosis in both ethnic groups, especially as the genetic benefit exhibited by black children to higher bone mass may be weakened with time, as environmental influences become stronger.