Aim. The objective of the study was to investigate iron status in children in relation to intake of cow's milk and follow-on formula. Methods. In all, 367 healthy 2.5-y-old children were enrolled in the study. The amounts of cow's milk and formula consumed were recorded. B-haemoglobin, S-ferritin, S-iron, total iron binding capacity and mean corpuscular volume were analysed. Results. Seven percent of the children had iron deficiency anaemia (Hb <110 g/l) and 10% had S-ferritin <12 μg/1. Furthermore, 10% of the children were iron deficient, with or without anaemia. Children with iron deficiency had a higher intake of cow's milk (382 ml, 95% confidence interval (CI) 294-496, vs. 257 ml, CI 232–272, p< 0.0001), and fewer consumed follow-on formula (11% vs. 43%, p = 0.0002) compared to those with sufficient iron. Conclusion. Iron deficiency is still common during childhood in Sweden. Intake of cow's milk is significantly higher in children with iron deficiency. In contrast, iron deficiency is less frequent among those consuming follow-on formula.