In the present study, the association between the CDKN2A-rs10811661 polymorphism and prediabetes was consistently significant when adding each of the obesity − related traits in the analysis models including age, gender, systolic blood pressure, socio-economic status and lifestyle factors, indicating the direct effect of the CDKN2A-rs10811661 polymorphism on prediabetes, independently of the obesity–related traits. Here, CDKN2A is linked to prediabetes syndrome.