BACKGROUND: A low-glycemic index (GI) diet may modulate adipocyte-produced adipokines linking to insulin resistance. METHODS: The stored plasma samples from the RCT of a low-GI vs. conventional diet in obese children were analyzed for adipokines: leptin, adiponectin, resistin, and visfatin. Their relationships with clinical outcomes were assessed. RESULTS: Fifty-two participants completed the 6-month intervention trial (mean age: 12.0 ± 2.0 years, 35 boys). Both groups had significantly decreased BMI z-scores from baseline whereas the low-GI group had significant reduction in fasting insulin and HOMA-IR. There were no differences in adipokines between the groups before and after the intervention. However, there was an association between baseline leptin and the change of fat mass index (FMI) but not the insulin resistance in both groups. The higher the baseline leptin was, the lower the changes were for FMI after the intervention. CONCLUSION: Despite no demonstrable effect of low-GI diet on plasma adipokines, the higher baseline leptin was correlated with lower reduction of fat mass. Leptin resistance may have a detrimental effect on the reduction of adiposity in obese children. Baseline leptin could be a useful predictor of the change in body composition in an obesity intervention trial. IMPACT: Leptin resistance may have a detrimental effect in reducing the adiposity in obese children. This study is the first of its kind to compare the plasma adipokine concentrations of obese children on low-GI diet and conventional diet. We found that serum leptin was significantly correlated with the reduction of BMI z-score and FMI in both groups. Baseline leptin could be a useful predictor of the change in body composition in an obesity intervention trial.