Bone biomarkers may be useful for examining the bone response to interventions in children. The purpose of this study was to determine the relationship between osteocalcin (OC), pyridinoline (PYD), and deoxypyridinoline (DPD) with changes in bone area (BA), bone mineral content (BMC), and bone mineral density (BMD) of the total body, lumbar spine, proximal femur, and radius in 32 prepubertal females over three years. Anthropometrics, maturation, calcium intake, and physical activity were also assessed. Osteocalcin, BA, BMC, and BMD at all sites increased significantly over time (p<0.0001). Annual increments of OC were significantly predicted by weight (slope = 0.305, p = 0.002), PYD by BMI (slope = 27.2, p = 0.002) and height (slope = 17.5, p = 0.046), DPD by BMI (slope = 3.52, p = 0.019). Bone biomarkers were not highly correlated to changes in bone variables. These results suggest that OC, PYD, and DPD are highly variable in children. Assessment of additional markers may be necessary to elucidate relationships between markers and changes in bone mass.