Studies investigating the relation between the focal nature of atherosclerosis and hemodynamic factors are employing increasingly rigorous approaches to map the disease and calculate hemodynamic metrics. However, no standardized methodology exists to quantitatively compare these distributions. We developed a statistical technique that can be used to determine if hemodynamic and lesion maps are significantly correlated. The technique, which is based on a surrogate data analysis, does not require any assumptions (such as linearity) on the nature of the correlation. Randomized sampling was used to ensure the independence of data points, another basic assumption of commonly-used statistical methods that is often disregarded. The novel technique was used to compare previously-obtained maps of lesion prevalence in aortas of immature and mature cholesterol-fed rabbits to corresponding maps of wall shear stress, averaged across several animals in each age group. A significant spatial correlation was found in the proximal descending thoracic aorta, but not further downstream. Around intercostal branch openings the correlation was borderline significant in immature but not in mature animals. The results confirm the need for further investigation of the relation between the localization of atherosclerosis and blood flow, in conjunction with appropriate statistical techniques such as the method proposed here.