BACKGROUND: Food allergy (FA) is a common disease in children, and its prevalence has increased in developed countries. The impact of overweight on children health also becomes an important social problem. However, the relationship between overweight and FA is still unclear. We examined the association between overweight and the prevalence of FA among Japanese children. METHODS: We analyzed data obtained using a self-administered questionnaire from 1772 Japanese children. Weight groups according to body mass index cutoff points proposed by the International Obesity Task Force were used to create two groups: overweight and non-overweight. Children were separated into four age groups (3-6 years, 6-9 years, 9-12 years, and 12-15 years) to examine age differences. We performed univariate and multivariate logistic models to examine the association between overweight and FA. RESULTS: The prevalence of FA was significantly higher in boys (10.6%, p = 0.014) than girls (4.5%) and girls (7.9%, p = 0.012) than boys (2.5%) for 6-9 and 12-15 age groups, respectively. While the prevalence of FA was significantly higher in overweight than non-overweight girls (26.1%, p = 0.005) in the 12-15 age group, no significant difference was found in boys. In girls, overweight was significantly associated with FA after adjustment for age and asthma (odds ratio 1.99, 95% confidence interval 1.01-3.89, p = 0.046). CONCLUSIONS: Our results showed that being overweight was significantly associated with a higher prevalence of FA in girls, but not in boys. Further prospective studies are necessary to find the causal relationship between overweight and FA.