Sirtuins (SIRTs) and Uncoupling Proteins (UCPs) have been implicated in atherosclerosis and cardiovascular disease through the control of reactive oxygen species production. We have previously shown that variations in SIRT and UCP genes are associated with increased risk for carotid plaque and carotid intima media thickness. Given that carotid arterial stiffness (STIFF) may be a biologically and genetically distinct phenotype of atherosclerosis, in the present study we extend our investigations to associations between genetic variation in the SIRT and UCP genes and STIFF. In a group of 1,143 stroke-free subjects with available high-definition carotid ultrasonography and genotyping, we investigated the association of 85 single nucleotide polymorphisms (SNPs) in 11 SIRT and UCP genes with carotid artery diameters, strain and STIFF. We also explored the effect modification of modifiable vascular risk factors on the associations SIRT and UCP genetic variants and STIFF and its components by interactions analysis. After adjustment for demographic and vascular risk factors, T allele carriers of rs10498683 in SIRT5 had greater STIFF (β = 0.07 per copy of T allele, P = 0.045), whereas G allele carriers of rs7895833 in SIRT1 had lower STIFF (β = −0.06 per copy of G allele, P = 0.027). SNPs in UCP1, UCP3 and UCP5 were associated with both diastolic and systolic diameters. Interactions with a nominal P < 0.005 were found between smoking and SNPs in SIRT1, and between diabetes and SNPs in SIRT5 in the associations with STIFF and carotid artery diameters. Genetic variation in UCP and SIRT genes are associated with carotid stiffness and their effect may be modified by modifiable vascular risk factors. The observed effect modifications by smoking and diabetes deserve further investigation.