There is evidence to suggest that IGF-I plays a role in regulating bone turnover. To evaluate the relationships between serum concentrations of IGF-I and IGF-binding protein-3 (IGFBP-3), and bone metabolism markers in healthy children. Prospective cross-sectional study. A cohort of 579 boys and 540 girls, all healthy Caucasian, were included in this study. Serum IGF-I and IGFBP-3 concentrations, bone alkaline phosphatase (BAP) and CrossLaps (markers of bone formation and bone resorption respectively) levels were evaluated as a function of age, gender, pubertal stage and body mass index. Serum IGF-I SDS levels were positively correlated with BAP and CrossLaps SDS levels before and after puberty, and also with CrossLaps during puberty (weak correlation). Serum IGFBP-3 SDS levels were positively correlated with BAP and CrossLaps levels before, during (weak correlation) and after puberty (for BAP levels only). This study demonstrated the independent association between serum IGF-I and IGFBP-3 concentrations with both serum bone formation and resorption markers in healthy children. Physiological differences before, during and after puberty in the association of serum IGF-I and IGFBP-3 levels with the serum bone metabolism markers were found. These differences may be related to differences in interactions between sex steroid hormones and the GH/IGF-I system, bone metabolism and growth during the pubertal transition. Improvements in our understanding of life course determinants of the IGF-I system and bone metabolism are required to shed further light on the role of the GH/IGF-I axis in bone remodelling.