Although the prevalence and causes of food allergy (FA) vary by geographic location, large well-designed epidemiological studies in Asia are lacking. The purpose of this study was to evaluate the prevalence of immediate-type FA in the general population of Korean schoolchildren. A population-based, cross-sectional study was conducted in 2010 using a stratified two-stage cluster-sampling design. In this survey, children aged 6-7 years and 12-13 years were randomly selected, and the presence of FA was determined by a questionnaire survey and assessment of specific IgE. After adjustment for missing data, 3907 children aged 6-7 years and 3975 students aged 12-13 years who completed the questionnaire were included in this study. In children aged 6-7 years, the prevalence of confirmed immediate-type FA was 0.3%, and the prevalence of possible immediate-type FA was 0.3%. By contrast, 0.6 and 1.0% of children aged 12-13 years had confirmed immediate-type FA and possible immediate-type FA, respectively. In 6- to 7-year-old children, egg was the most frequent causative food associated with a confirmed or possible immediate-type FA. In 12- to 13-year-old children, crustaceans were the most frequent cause of confirmed immediate-type FA, and fruit was most frequently involved in possible immediate-type FA. This is the first nationwide population-based study of FA in Korean schoolchildren. Unlike in western countries, the prevalence of immediate-type FA seems to be low. In 12- to 13 year-old children with confirmed immediate-type FA, peanuts/tree nuts are not common causes, whereas crustaceans are frequent triggers.