Intra-luminal thrombus has been suggested to play a role in the progression of abdominal aortic aneurysm (AAA). The aims of this study were twofold. Firstly, to assess the reproducibility of a computer tomography (CT)-based technique for measurement of aortic thrombus volume. Secondly, to examine the determinants of infrarenal aortic thrombus volume in a cohort of patients with aortic dilatation. A consecutive series of 75 patients assessed by CT angiography with maximum aortic diameter > or = 25 mm were recruited. Intra-luminal thrombus volume was measured by a semi-automated workstation protocol based on a previously defined technique to quantitate aortic calcification. Intra- and inter-observer reproducibility were assessed using correlation coefficients, coefficient of variation and Bland-Altman plots. Infrarenal aortic thrombus volume percentage was related to clinical, anatomical and blood characteristics of the patients using univariate and multivariate tests. Infrarenal aortic thrombus volume was related to the severity of aortic dilatation assessed by total aortic volume (r = 0.87, P < 0.0001) or maximum aortic diameter (r = 0.74, P < 0.0001). We therefore examined the clinical determinates of aortic thrombus expressed as a percentage of total aortic volume. Aortic thrombus percentage was negatively correlated with serum high density lipoprotein (HDL, r = -0.31). By ordinal multiple logistic regression analysis serum HDL below median (< or = 1.2 mM: ) was associated with aortic thrombus percentage in the upper quartile adjusting for other risk factors (odds ratio 5.3, 95% CI 1.1-25.0). Infrarenal aortic thrombus volume can be measured reproducibly on CT. Serum HDL, which can be therapeutically raised, may play a role in discouraging aortic thrombus accumulation with implications in terms of delaying progression of AAA.