We previously reported that high intake of milk, but not meat, equal in protein content, increased serum insulin-like growth factor-I (sIGF-I) in prepubertal boys. sIGF-I plays a key role in bone metabolism. Therefore, the aim of this cross-sectional study was to investigate associations of total, dairy, and meat protein intake with markers for bone turnover and sIGF-I in prepubertal, healthy boys (n = 81). We measured bone turnover (enzyme-linked immunoassay) in serum osteocalcin (sOC), bone-specific alkaline phosphatase (sBAP), and C-terminal telopeptide of collagen type-I (sCTX); dietary intake was estimated from a 3-d weighed food record. sIGF-I and its binding protein-3 were assessed (immunoassay) in a subgroup of 56 boys. All statistical models included effects of age, BMI, and energy intake. Dairy protein was negatively associated with sOC (P = 0.05) but not significantly associated with sBAP and sCTX. Further analyses showed that dairy protein decreased (P = 0.05) sOC at a high meat protein intake (>0.8 g/kg), whereas meat protein increased (P = 0.03) sOC at a low dairy protein intake (<0.4 g/kg). Total and meat protein intake was positively associated with sBAP (P < or = 0.04) but not significantly associated with sOC and sCTX. Free sIGF-I was positively associated with total (P < 0.01) and dairy (P = 0.06) protein but not with meat protein. Our results indicate that dairy and meat protein may exhibit a distinct regulatory effect on different markers for bone turnover. Future studies should focus on differential effects of dairy and meat protein on bone health during growth.