The present study aimed to investigate the distribution of total serum immunoglobulin E (IgE) levels in Korean schoolchildren and to evaluate its utility in the prediction of atopy and allergic diseases. A nationwide, cross-sectional survey was conducted in first grade students from randomly selected elementary and middle schools. Total IgE levels were measured by ImmunoCAP. Skin prick tests were performed for 18 common inhalant allergens to determine the presence of atopy. Children aged 12–13 years and parents of children aged 6–7 years were asked to complete questionnaire assessing allergic diseases. The cut-off levels of total IgE were determined by analyzing receiver operating characteristic curves. The median total IgE level was 86.7 kU/L (range: 1.5–4,523.1) in 3,753 children aged 6–7 years and 94.7 kU/L (range: 1.5–3,000.0) in 3,930 children aged 12–13 years. Total IgE concentrations were higher in children with atopy or allergic diseases than in those without (all P < 0.001). At the cut-off value of 127.7 kU/L, sensitivity, specificity, and positive and negative predictive values (PPV and NPV) were 67.1%, 75.4%, 65.4%, and 76.7%, respectively, in elementary schoolchildren. At the cut-off value of 63.0 kU/L, sensitivity, specificity, PPV, and NPV were 81.9%, 66.6%, 75.0%, and 75.1%, respectively, in middle schoolchildren. PPV and NPV were ≥ 70% when cut-offs of 258.8 kU/L and 38.4 kU/L were used for the diagnosis of atopy in 6–7 year-olds and 12–13 year-olds, respectively. This nationwide population-based study provided the first normal reference ranges of total IgE in Korean schoolchildren.