Patients with active juvenile idiopathic arthritis (JIA) have frequently low haemoglobin (Hgb) due to inflammation and/or iron deficiency. The aim of the study was to evaluate the effect of anti-tumor necrosis factor (TNF) therapy on their iron status. Twenty children with JIA were treated with either etanercept (n = 8) or infliximab (n = 12) for 12 months. Iron status was assessed during anti-TNF treatment by Hgb, mean corpuscular volume of red blood cells (MCV), serum iron (sFe), ferritin, percent transferrin saturation (sTrfesat) and serum transferrin receptor concentration (sTfR). The sTfR/log ferritin index (TfR/logF) was also used. Prior to the therapy, Hgb and MCV were 118 ± 15.5 g/L and 79 ± 7.7 fl in the infliximab group, and 113 ± 12.5 g/L and 78 ± 5.8 fl in the etanercept group, respectively. In the whole group of patients, sFe was 6.3 ± 4.1 μmol/L and sTrfesat was 9% ± 6%. During anti-TNF therapy, Hgb and MCV improved significantly without use of iron supplementation, and sFe and sTrfesat increased from low to normal levels while inflammation markers decreased, except in one patient, in whom sTfR stayed elevated and the TfR/logF index value was high. In patients with active JIA associated with anaemia, low levels of sFe and sTrfesat cannot be used as markers for iron deficiency. In such patients, sTfR together with TfR/logF seem to be useful in assessing iron deficiency.