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Objective Adolescents with prediabetes are at high risk of developing type 2 diabetes in later life. It is necessary to identify risk factors for prediabetes in adolescents. This study aimed to examine the association between skipping breakfast and prediabetes among adolescents in Japan. Study design We used the population-based cross-sectional data of eighth grade in junior high school students from the Adachi Child Health Impact of Living Difficulty (A-CHILD) study conducted in Adachi City, Tokyo, Japan, in 2016, 2018, and 2020. Skipping breakfast was assessed using self-reported questionnaires (N=1510). Prediabetes was defined as hemoglobin A1c (HbA1c) levels of 5.6-6.4%. The association between skipping breakfast and prediabetes was evaluated using multivariate logistic regression analysis. Stratified analysis was also performed using BMI, 1 SD or more, or less than 1SD, as overweight was defined as 1SD or more. Results Students who skipped breakfast were 16.4% (n=248). The prevalence of prediabetes was 3.8% (n=58). Skipping breakfast exhibited a significant association with prediabetes (OR:1.95, 95% CI: 1.03 to 3.69) after adjusting for sex, annual household income, family history of diabetes mellitus, BMI, and survey year. Stratified analysis showed stronger association among students with overweight (BMI ≥1SD) (OR=4.31, 95% CI 1.06-17.58), while non-sigificant among students without overweight (BMI<1SD) (OR=1.62, 95% CI 0.76-3.47). Conclusions Skipping breakfast in Japanese adolescents, especially those with overweight, was associated with prediabetes. The promotion of avoiding skipping breakfast may help to prevent prediabetes.