Purpose: The aim of this study was to compare bone mineral density (BMD) in adolescent male basketball (BB) and soccer (S) players. Methods: The study included Estonian national youth league level participants: 12 BB (16.3 ± 0.7 years, 186.8 ± 6.6 cm, 80.9 ± 11.9 kg) and 15 S players (16.0 ± 0.3 years, 178.5 ± 8.1 cm, 66.3 ± 6.8 kg). All participants had a history of 7.9 ± 2.9 years of training, with training loads of 9.2 ± 1.8 h per week. Body composition and BMD were determined by dual X-ray absorptiometry (DXA). Results: BB were significantly taller, heavier and had greater lean body mass (LBM) compared to S. No significant (P < 0.05) differences existed in age, body fat %, sports participation, and weekly training load. BB had significantly (P < 0.05) greater BMD values in total body, lumbar spine, right arm, left arm, right leg, right femur, right femoral neck, and right femoral shaft compared to S. The biggest between-groups difference (P < 0.001) existed in upper extremities (25–28%). LBM was the main determinant for all BMD variables. Conclusions: Regular participation in basketball and soccer practice in adolescent males is associated with enhanced BMD in loaded sites specific to demands of the sport. Basketball practice seems to have higher impact on non-weight bearing bones, compared to soccer. © 2016, Springer-Verlag Italia.