Objectives The aim of this study was to determine whether weight training combined with high-protein intake enhances total and regional bone mineral density (BMD) in athletes. Methods BMD of 27 Division 1 collegiate baseball players 18 to 22 y of age (N = 13, 2 dropouts) received either 14% protein or isocaloric 44% protein supplements and were assessed by dual-energy x-ray absorptiometry before and after a 12-wk weight training program (challenging upper and lower body). Results Baseline data showed unequivocally greater humerus BMD in the dominant arm than their contralateral non-dominant arm (∼20 %) among all baseball players. Humerus BMD of the non-dominant arm was enhanced by 2.7% after weight training for both low- and high-protein groups (main effect, P = 0.008), concurrent with an unexpected small decrease in total body BMD (main effect, P = 0.014). Humerus BMD of the dominant arm with greater baseline value than the non-dominant arm was not increased unless high protein was supplemented (+2.7 %; P < 0.05). Conclusion Bones with relatively higher BMD show blunt adaptation against training, which can be relieved by high-protein supplementation. Total BMD of athletes cannot be further elevated by weight training.