Serum soluble transferrin receptors (sTfR) concentration is a useful test in the diagnosis of childhood iron deficiency (ID). The aims of this study were to establish reference limits and to evaluate the diagnostic characteristics of sTfR in the diagnosis of ID in infants aged 9-12 months. In addition to mean erythrocyte cell volume, haemoglobin and ferritin measurements, sTfR concentration was measured in 179 healthy children in Estonia using the IDeA and Tina-quant methods. Using the ID criteria of ferritin <10 microg/l, subjects were divided into healthy (n = 146) and ID (n = 33) groups. The reference limits (5th and 95th percentile) were calculated in the study group. We used receiver operating characteristic curves to find out the cut-off values for the best diagnostic characteristics. The reference limits for sTfR were 1.5-2.7 mg/l in the IDeA method and 4.1-7.8 mg/l in the Tina-quant) method. The methods had poor agreement, the mean ratio with 95% limits of agreement was 2.9 (2.4-3.6). The best cut-off value in order to identify ID by hypoferritinaemia in this population is an sTfR level > 2.4 mg/l in the IDeA (sensitivity 84%, specificity 94%) and an sTfR level > 7.4 mg/l in the Tina-quant (sensitivity 80%, specificity 92%). We conclude that sTfR concentration is an efficient tool in the diagnosis of ID, but that every method needs its own cut-off value.