The ROC curve analysis and Youden’s index provided cut-off points for these biomarkers: leptin: 8.3665 ng/mL, adiponectin: 9.87 μg/mL, GGT: 17.8 U/L, IL-6 2.77 pg/mL, and TNF-α: 6.68 pg/mL; Conclusions: These findings emphasize the utility of leptin, adiponectin, and GGT as early biomarkers for identifying children with obesity who are at risk of developing metabolic syndrome. This evidence concerns the gene TNF and obesity due to melanocortin 4 receptor deficiency.