To assess body composition by means of BOD POD in the large cohort of Italian Olympic athletes of many sport disciplines (studied at the same time), and to provide possible reference values for body composition in elite athletes. 1556 elite athletes, who took part in the selection procedure for the 2016 Rio Olympic Games for the National Italian Olympic Committee (CONI), were retrospectively studied. Body composition was determined using air plethysmography-based BOD POD. We observed that Fat Mass (FM) and Fat-free Mass (FFM) should be considered as two mutually independent domains in elite athletes. By performing Principal Component Analysis, we defined two independent main domains (respectively, representing FM and FFM), which presented different trends according to gender and static or dynamic exercise load. Lastly, we reported possible reference values for FM index and FFM index, respectively, representing the largest contributors to FM domain and FFM domain, and calculated as FM or FFM (kg)/height (m2). Our findings might provide a basis to optimize the practical approach to body composition in athletes, highlighting the importance of considering indicators of fat mass and lean mass "simultaneously" and not specularly, according to different sport disciplines as well. Moreover, these data might contribute to standardize reference values for body composition in elite athletes, with a view to potentially helping to monitor and guide training regimens, prevent related detrimental practices and plan cardiometabolic prevention and rehabilitation programs.