BACKGROUND Data concerning the relationship between body fat and BMD are equivocal since both positive and negative effects have been noted. Recently, the index of fat mass (IFM) representing subjects with different body fat and similar lean mass and index of lean mass (ILM) representing subjects with different lean body mass and similar body fat, have been used to evaluate body composition effect on BMD in middle-aged women. This study aimed at determination of ILM and IFM association with BMD in young men and women. METHODS A total of 212 university students of Public Health (125 women and 87 men) participated in the study. Body composition was determined by the bioelectrical impedance method (BIA) using BC 418 MA equipment (Tanita Co., Japan). Fat mass and fat free mass were used to calculate ILM and IFM. Bone mineral density was measured on the wrist of the non-dominant hand using the DEXA method and EXA 3000 equipment (HFS Ltd., Korea). BMD was evaluated using Z-score, with values lower than -2.0 indicating inadequate BMD for subject chronological age. RESULTS Exclusively in women, IFM was markedly and positively correlated with Z-score (r=0.366, P<0.001). In both genders, a significant relationship was found between ILM and Z-scores (r=0.420; p<0.001 and r=0.220; p<0.02 in men and women, respectively). Women with lower than median IFM but similar ILM, were characterized by significantly lower Z-scores vs. women with higher IFM (-1.016 vs. -0.512; p<0.001). Irrespective of gender, participants with higher ILM but similar IFM, were characterized by markedly higher Z-score vs. their counterparts with low ILM. CONCLUSIONS The use of IFM and ILM in the present study, allowed the observation that in young adults lean body mass was associated with BMD, regardless of gender, while fat mass is significant for bone mineral density only in women.