The effects of dietary protein on Ca bioavailability and utilization in bone were examined in male spontaneously hypertensive rats (SHR) fed on diets containing either casein (200 g/kg (control), 60 g/kg or heat-damaged (HD) 200 g/kg) or soya-bean protein isolate (200 g/kg (control), 60 g/kg, or HD 200 g/kg). Casein was heat-damaged to limit caseinophosphopeptide (CPP) production in order to evaluate casein enhancement of Ca bioavailability. All diets contained an adequate level of Ca (5 g/kg). A 24 h mineral balance study was performed when animals were 10 weeks old, followed by measurement of in situ paracellular Ca disappearance, femur mineralization and biomechanics at 14 weeks of age. Digestibility of soya-bean and both HD proteins estimated in vitro was reduced compared with native casein. Animals fed on HD and 60 g/kg protein diets exhibited decreased (P < 0.05) body weight gain, dry matter intake and feed efficiency compared with controls. The ileal disappearance of 45Ca was lower (P < 0.05) in animals fed on HD casein and all the soya-bean protein diets. Ca balance was not strongly affected by dietary treatments. A significant (P < 0.05) interaction between protein source and reduced protein intake was observed for femur calcification and physical measurements. Femur bending failure energy and biomechanical force measurements were reduced (P < 0.05) in HD and 60 g/kg casein and soya-bean protein fed animals. These findings suggest that whole-body Ca homeostatic mechanisms were involved in compensating for reduced Ca bioavailability and retention from casein diets modified to reduce protein digestibility and CPP production.