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Pro12Ala variant of peroxisome-proliferator-activated receptor-gamma2 (PPAR-gamma2) may be linked to insulin sensitivity. This study examined whether an association of PPAR-gamma2 Pro12Ala with insulin resistance and plasma LCPUFAs may exist in obese children. One hundred and forty Italian normolipidemic obese children (58 girls and 82 boys, mean age [SD], 10.2 [2.7] y) entered the study. Obesity was defined according to International Obesity Task Force. BMI Z-scores were calculated. Fasting blood glucose, insulin, lipids and plasma fatty acids were measured. Insulin resistance was estimated by the homeostatic model assessment (HOMA-IR). The frequency of Ala allele was 9%. Mean [SD] values of fasting insulin and HOMA-IR in Pro/Pro versus Pro12Ala groups were: 19.3 [10.6] versus 14.1 [10.4] microU/mL (p = 0.017) and 4.2 [2.3] versus 3.0 [2.3] (p = 0.022). Mean [SD] values of plasma C20:3n-9 and of C20:4n-6, C20:5n-3, C22:6n-3 and n-6/n-3 LCPUFA in phospholipds in Pro/Pro versus Pro12Ala groups were: 0.15 [0.07] versus 0.12 [0.08] % (p = 0.014), 8.9 [1.9] versus 10.2 [2.6] % (p = 0.023), 0.34 [0.15] versus 0.42 [0.11] % (p = 0.005), 2.1 [0.9] versus 2.6 [0.9] % (p = 0.032) and 4.8 [1.2] versus 4.2 [0.7] (p = 0.017). Pro12Ala may be associated with higher insulin sensitivity and higher LCPUFAs, particularly n-3, levels in plasma phosholipids of obese children.