We examined the role of UCP gene polymorphisms as susceptibility markers for premature coronary artery disease (pCAD). The UCP2 Ala55Val ( C/T rs660339), UCP2 -866G/A (rs659366), and UCP3 - 55C/T (rs1800849) polymorphisms were genotyped in 948 patients with pCAD, and 763 controls. The distribution of the UCP2 A55V ( C/T rs660339) and UCP3 -55 (rs1800849) was similar in patients and controls. However, under a recessive model, the UCP2 -866 (rs659366) A allele was associated with increased risk of developing pCAD (OR = 1.43, Pc = 0.003). On the other hand, patients with pCAD and UCP2 A55V (rs660339) TT showed high levels of visceral abdominal fat (VAF) ( Pc = 0.002), low levels of subcutaneous abdominal fat (SAF) ( Pc = 0.001) and high VAT/SAT ratio ( Pc < 0.001). Also, patients with UCP2 -866 (rs659366) AA showed increased levels of VAF ( Pc = 0.003), low levels of SAF ( Pc = 0.001) and a high VAT/SAT ratio ( Pc = 0.002), whereas patients with the UCP3 -55 (rs1800849) TT presented high levels of VAF ( Pc = 0.002). The results suggest the association of the UCP2 -866 (rs659366) polymorphism with risk of developing pCAD. Some polymorphisms were associated with abdominal fat levels and cardiovascular risk factors.