Increased consumption of Trans Fats is associated with increased risk of Coronary Heart Disease. Uncoupling proteins (UCPs) are mitochondrial proteins that disperse the inter-membrane electrochemical potential as heat. We aimed to detect the relation of high Trans-fat intake in diet on the expression of UCP2&3 m-RNA in children. A specific questionnaire to parents of sixty-eight children (4-15 years) was conducted. Accordingly, the subjects were sub-grouped into; High Trans-fat consuming group (37 subjects) and a Medium Trans-fat consuming one (31 subjects). Samples collected from Peripheral blood to analyze UCP2&3 mRNA expression by Real Time Polymerase Chain Reaction (RT-PCR). Levels of UCP2 expression was reduced in children consuming High Trans-fat (2.5 ±0.7) in comparison with Medium Trans-fat consuming ones (1.5± 0.2) with (p<0.001). However, not much significance was showed in UCP3 expression with values (2.1±0.5) in the High consuming group and (1.9±0.2) in Medium consuming group with (p=0.08). In Delta relationship the diet-induced changes in UCP2 (r=0.66, P=0.002) and UCP3 (r=0.61, P=0.06) mRNA expression was negatively correlated with percentage of Trans-fat in diet. The correlation of UCP2&3 mRNA expression and high Trans-fat intake suggests a mechanism by which high Trans-fat diet plays a role in childhood obesity.