The purpose of this study was to determine which differences in the source of protein (soy vs casein) and isoflavones in soy protein are responsible for the differential effects of bone marks and hormones in growing female rats. Forty-two 21-day-old Sprague-Dawley female rats were randomly assigned to one of three groups, consuming casein (control group), soy protein isolate (57 mg isoflavones/100 g diet), or soy protein concentrate (about 1.2 mg isoflavones/100 g diet). All rats were fed on experimental diet and deionized water ad libitum for 9 weeks. Bone formation was measured by serum osteocalcin and alkaline phosphatase (ALP) concentrations. And bone resorption rate was measured by deoxypyridinoline (DPD) crosslinks immunoassay and corrected for creatinine. Serum osteocalcin, growth hormone, estrogen and calcitonin were analyzed using radioimmunoassay kits. Diet did not affect weight gain and mean food intake. Food efficiency ratio was lower in the soy protein groups. The soy isolate group had a higher ALP and osteocalcin concentration and lower crosslinks value than the casein group. Therefore, the soy isolate groups had a higher bone formation/resorption ratio than the casein group. And, the soy group had significantly higher growth hormone than the casein group. The findings of this study suggest that soy protein and isoflavones are beneficial for bone formation in growing female rats. Therefore, exposure to these soy protein and isoflavones early in life may have benefits for osteoporosis prevention.