In this paper we propose a methodology for predicting the progression of atherosclerosis in coronary arteries using dynamic Bayesian networks. The methodology takes into account patient data collected at the baseline study and the same data collected in the follow-up study. Our aim is to analyze all the different sources of information (Demographic, Clinical, Biochemical profile, Inflammatory markers, Treatment characteristics) in order to predict possible manifestations of the disease; subsequently, our purpose is twofold: i) to identify the key factors that dictate the progression of atherosclerosis and ii) based on these factors to build a model which is able to predict the progression of atherosclerosis for a specific patient, providing at the same time information about the underlying mechanism of the disease.