The purpose of this study was to determine to which differences in the source of protein (soy vs casein) and of isoflavones in soy protein are responsible for differential effects of bone mineral density and bone mineral content. Thirty 21-d-old Sprague-Dawley young rats were divided into 3 groups: the control group was find a casein-based diet, the soy concentrate group was fed soy protein with totally reduced isoflavones content (isoflavone 0.07 mg/g protein), and soy isolate group was fed with a higher isoflavone content (isoflavone 3.4 mg/g protein) than normal. The animal was scanned to determine the BMD and BMC using dual energy X-ray absorptiometry (DEXA, Lunar Corporation, Madison, WI). The soy concentrate group had significantly higher total body calcium/weight and total mineral content/weight than the casein group. The soy isolate group had significantly greater total bone mineral density/weight, spine bone mineral density/weight, and femoral bone mineral density (in g/$ extrm{cm}^2$ than the control and soy concentrate group. The findings of this study suggest that soy protein and isoflavones in soy protein are beneficial for bone-formation in growing male rats. Therefore exposure to these soy protein and isoflavones early in life may have long-term health benefits for bone diseases such as osteoporosis.