BACKGROUND: Some small cohort studies have noted that obesity co-exists with lower serum iron levels. The present study aimed to examine the association between being overweight and iron deficiency (ID) in a large cohort of Greek children and adolescents. METHODS: A representative sample of 2492 primary schoolchildren aged 9-13 years old was examined. Anthropometric, biochemical, clinical, dietary intake and physical activity data were collected. RESULTS: The prevalence of ID and iron deficiency anaemia (IDA) was higher in obese boys and girls compared to their normal-weight peers (P < 0.05). Serum ferritin was higher in obese compared to normal-weight boys (P = 0.024) and higher in obese compared to normal-weight and overweight girls (P = 0.001). By contrast, a negative association was found between transferrin saturation and adiposity in both boys and girls (P = 0.001 and P = 0.005). Furthermore, obese girls had significantly higher fibre intake than normal-weight girls (P = 0.048) and also overweight and obese boys and girls recorded significantly fewer pedometer steps than their normal-weight peers (P < 0.001). Finally, obesity more than doubled the likelihood of ID in both boys (odds ratio = 2.83; 95% confidence inteval = 1.65-4.85) and girls (odds ratio = 2.03; 95% confidence interval = 1.08-3.81) after controlling for certain lifestyle and clinical indices as potential confounders. CONCLUSIONS: The present study shows that obese children and adolescents were at greater risk for ID and IDA than their normal-weight peers. Low grade inflammation induced by excessive adiposity may be a reason for the observed low iron levels. This is also strengthened by the elevated serum ferritin levels, comprising an acute phase protein that is plausibly increased in inflammation.