Iron depletion seems to occur more frequently among athletes than in the general population and may affect performance capacity. Only little information is available about the prevalence of iron status abnormalities in young elite athletes and whether iron depletion is associated with gender, sport, age or nutrition- and exercise-related factors in this group. Hence, diet, exercise and haematological data from 193 elite athletes (96 males, 97 females; 16.2 ± 2.7 years) from 24 different sports were analyzed retrospectively. Most female athletes failed to meet the recommended daily allowance for iron, even though dietary iron density was higher than in males (5.75 ± 0.78 vs. 6.17 ± 0.98 mg/1,000 kcal; P = 0.001). Iron depletion (serum ferritin < 35 μg/L) occurred in 31% of male and 57% of female athletes (P < 0.001). Low haemoglobin (males: <13 g/dL; females: <12 g/dL) and haematocrit (males: <40%; females: <36%) values were equally prevalent in both genders [haemoglobin: 7.3% (males), 6.2% (females); haematocrit: 13.5% (males); 15.5% (females)]. In females, reduced ferritin levels were associated with a lower dietary iron density (5.9 ± 0.8 vs. 6.6 ± 1.1 mg/1,000 kcal; P = 0.002). Males with iron depletion had a significantly higher estimated energy expenditure (48.7 ± 7.0 vs. 44.4 ± 7.6 kcal/kg/day; P = 0.009).