Milk is a good source of bioavailable calcium compared with other foods. Recent in vitro and in vivo studies have shown that milk whey protein, especially its basic protein fraction (milk basic protein, MBP), contains several components capable of promoting bone formation and inhibiting bone resorption. The objective of this study was to examine the effects of MBP on bone mineral density (BMD) and bone metabolism of healthy young women. Eighty-four healthy young women were randomly assigned to three groups: control group, whole milk group or MBP group treated with milk containing 40 mg MBP for 8 months. The bone mineral density of total body, the lumbar vertebrae L2-L4 and the left forearm of each subject were measured by dual-energy X-ray absorptiometry (DEXA) at 0 and 8 months of treatment. Serum indexes of bone metabolism were measured at 0, 3, 6 and 8 months. Eighty-one subjects who completed the study in accordance with the protocol were included in the analysis. Total BMD in all groups significantly increased compared with baseline values. However, no significant difference on the mean rate of gain of total BMD was observed among the MBP group (2.19%), the whole milk group (2.63%) and the control group (1.61%). Serum cross-linked N-teleopeptides of type-I collagen (NTx) in MBP group at 8 months and in whole milk group at 6 months were significantly decreased from baseline. There were no significant differences between whole milk group and MBP group; however, after combining the milk groups, NTx had significantly decreased from baseline. No significant increase was observed in serum bone-specific alkaline phosphatase (BAP) in both whole milk group and MBP group. No significant effect of MBP on bone mineral density and bone metabolism was observed, but milk supplementation was effective in suppressing bone resorption.