Introduction: Cardiovascular diseases (CVDs) are responsible of 31% of all deaths worldwide. Genetic predisposition to CVDs in adolescents remains largely unknown. Objective: To examine the association of UCP1, UCP2 and UCP3 gene polymorphisms with CVDs risk factors in European adolescents. Study design: A cross-sectional study that involves 1.057 European adolescents (12-18 years old) from the HELENA Study. A total of 18 polymorphisms of UCP1, UCP2 and UCP3 genes were genotyped. We measured serum total cholesterol, HDL, ApoA1, ApoB, leptin, triglycerides, glucose, insulin, blood pressure, and calculated HOMA (homeostatic model assessment) and a CVD Risk Score. Results: The G allele of UCP2 rs2735572 and T allele of UCP2 rs17132534 were associated with higher diastolic blood pressure (P=0.001; FDR=0.009 and P=8e−04; FDR=0.009, respectively). We observed that the AATAG haplotype of UCP1 was associated with higher serum ApoB/ApoA1 (P= 0.008; FDR = 0.031) and ApoB levels (P= 0.008; FDR = 0.031). Moreover, the ACC haplotype of UCP3 was associated with a higher CVD risk score (P= 0.0036; FDR = 0.01). Conclusions: Two UCP2 polymorphisms and haplotypes of UCP1 and UCP3 were associated with CVD risk factors. These findings suggest that UCPs may have a role in the development of CVD already in adolescents.