Carotid-femoral pulse wave velocity (PWV), a measure of central arterial stiffness and carotid intima-medial thickness (CIMT), thought to be a measure of subclinical atherosclerosis, are predictors of future cardiovascular events, recommended for risk stratification. Their relationship, however, remains poorly characterised. We sought to determine the association between PWV, CIMT and atherosclerotic plaque at the carotid and femoral artery and the heritability of PWV and CIMT. The study population consisted of 496 female twins (112 monozygotic (MZ), 135 dizygotic (DZ), mean age (interquartile range) 58 (53–64) years, from the TwinsUK cohort. PWV was determined using the SphygmoCor system (Atcor Australia) and CIMT measured 1 cm proximal to the flow divider by B-mode ultrasound. Plaque was quantified according to its presence at the carotid and femoral artery. Multiple regression analysis was used to examine the relation between PWV, CIMT and plaque. Heritability was determined from intra-class correlations. In multiple regression analysis incorporating age, mean arterial pressure (MAP) and heart rate (HR), PWV was not significantly positively correlated with CIMT, indeed there was a weak but significant negative correlation between PWV and CIMT (standardised regression coefficient β=−0.13, P<0.05). PWV was weakly positively associated with plaque (β=0.13, P<0.01). Heritability of PWV (adjusted for HR and MAP) and CIMT (adjusted for MAP, total cholesterol and HDL-cholesterol) was 0.34 and 0.57 respectively. These results confirm high heritability of CIMT but suggest that it is largely independent of PWV which may be influenced more by environmental factors. Combining measures of CIMT and PWV might improve risk stratification.