The aim of the present study was to examine the associations of obesity, percentage body fat and visceral fat mass with body Fe status in a representative sample of 1493 schoolchildren aged 9–13 years. Anthropometric, body composition, biochemical, clinical (Tanner stage, age of menarche) and dietary intake data were collected. Fe deficiency (ID) was defined as transferrin saturation (TS) < 16 %; and Fe-deficiency anaemia (IDA) as ID with Hb < 120 g/l. Obese boys and girls and those in the highest quartiles of percentage body fat mass had significantly higher levels of serum ferritin (P ≤ 0·05) compared to their normal-weight peers and those in the corresponding lowest quartiles. Similarly, obese boys and girls and those in the highest quartiles of percentage body fat and visceral fat mass had significantly lower levels of TS (P ≤ 0·05) compared to normal-weight children and those in the corresponding lowest quartiles. The prevalence of ID and IDA was significantly higher in boys and girls in the highest quartiles of percentage body fat than in peers in the lowest quartile. Higher quartiles of percentage body fat and visceral fat mass were the main significant predictors of ID in boys, after controlling for other important confounders, with OR of 2·48 (95 % CI, 1·26, 4·88) and 2·12 (95 % CI, 1·07, 4·19), respectively. Similar significant associations were observed for girls. In conclusion, percentage body fat and visceral fat mass were positively associated with ID in both sexes of preadolescents. These associations might be attributed to the chronic inflammation induced by excess adiposity.