Background. This study investigated the association between insulin resistance (IR) and metabolic syndrome (MetS) in children. Methods. A cross-sectional study involving 1036 healthy children aged between 7 and 13 years was conducted. Homeostasis model assessment of insulin resistance (HOMA-IR) was calculated as an index of IR. Participants were classified according to the HOMA-IR quartiles. Results. Incremental, linear trends were found in age (p < 0.001), body mass index (BMI) (p < 0.001), body fat (p < 0.001), waist circumference (p < 0.001), resting blood pressures (BP) (p < 0.001), triglycerides (TG) (p < 0.001), total cholesterol (TC) (p < 0.001), high density lipoprotein-cholesterol (HDL-C) (p < 0.001), FBG (p < 0.001), and insulin (< 0.001) according to incremental HOMA-IR categories (from the 1st to 4th quartile). Compared with children in the 1st HOMA-IR quartile, children in the 4th HOMA-IR quartile had significantly higher odd ratios (ORs) of abnormalities in systolic (p = 0.051) and diastolic BP (p = 0.005), FBG (p < 0.001), TG (p < 0.001), TC (p = 0.016), and HDL-C (p = 0.006) even after adjustments for age, gender, BMI, and body fat percentage. Children in the 3rd HOMA-IR quartile had significant abnormalities in FBG (p < 0.001), TG (p = 0.001), and HDL-C (p = 0.010) even after adjustments for the covariates. Conclusion. The current findings suggest that IR is significantly associated with the clustering of MetS risk factors in children in Korea.