In children, 90% of all anemia cases are due to iron deficiency. Iron is an essential element so iron metabolism disorders have negative consequences for health. Currently, there are no reliable statistical data on the prevalence of iron deficiency in elite young athletes in the Russian Federation (RF). The aim of this study was to evaluate the prevalence of iron deficiency anemia (IDA) and latent iron deficiency (LID) in young elite athletes. We retrospectively analyzed 802 outpatient records of members of the Russian national sport teams aged 13–18 (mean age is 15.4 ± 2.1 years; 434 (54.1%) girls, 368 (45.9%) boys) in 17 sports, who underwent indepth medical examination including clinical blood tests and serum iron level assays. IDA was diagnosed in 43 young elite athletes (5.4% of all examined athletes). The prevalence of IDA in female adolescents was significantly higher than in male adolescents (8.9% and 1.1%, respectively; p = 0.0001). The prevalence of LID in game sports was significantly higher compared to the other sports. LID was recorded in 186 athletes (23.2%). LID was less common in cyclic sports and was not gender dependent. It can be concluded that young elite athletes have a moderate prevalence of IDA (> 5%). However, since LID was diagnosed in 20% of the athletes, it may be necessary to perform thorough examination for timely screening and correction of iron deficiency in adolescent high performance sports.