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The associations between individual components of metabolic syndrome (MetS) and bone health in children are complex, and data on this topic are sparse and inconsistent. We assessed the relationship between bone turnover markers and markers of the processes underlying MetS (insulin resistance and inflammation) in a group of presumably healthy children aged 9–11 years: 89 (51 girls, 38 boys) presenting without any features of MetS and 26 (10 girls, 16 boys) with central obesity and two features of MetS. Concentrations of glucose, triglycerides (TG), HDL cholesterol (HDL-C), C-reactive protein (CRP), HbA1c, total 25-hydroxyvitamin D (25(OH)D), intact-P1NP (N-terminal propeptide of type I procollagen), CTX-1 (C-terminal telopeptide of type I collagen) were assayed and insulin resistance was assessed (HOMA-IR). BMI centile, waist circumference (WC) and blood pressure were measured. The presence of MetS in girls resulted in significantly lower concentrations of CTX-1 and a trend to lower CTX-1 in boys. The concentrations of bone formation marker i-P1NP were not affected. Among the features associated with MetS, HOMA-IR appeared as the best positive predictor of MetS in girls, whereas CRP was the best positive predictor in boys. A significant influence of HOMA-IR on the decrease in CTX-1 in girls was independent of BMI centile and WC, and the OR of having CTX-1 below the median was 2.8-fold higher/1SD increased in HOMA-IR (p = 0.003). A weak relationship between CTX-1 and CRP was demonstrated in girls (r = −0.233; p = 0.070). Although TG, as a MetS component, was the best significant predictor of MetS in both sexes, there were no correlations between bone markers and TG. We suggest that dyslipidemia is not associated with the levels of bone markers in prepubertal children whereas CRP is weakly related to bone resorption in girls. In prepubertal girls, insulin resistance exerts a dominant negative impact on bone resorption, independent of BMI centile and waist circumference.