The problem of atherosclerosis, which forms the pathological basis of coronary artery disease (CAD), is one of the most discussed ones in development of cardiovascular diseases. This chronic inflammatory disease involves interactions between different cells, and an atherosclerotic plaque is a complex immunological environment. Modern quantitative methods increase the understanding of the pathophysiological processes responsible for progression of atherosclerotic plaques. Flow cytometry is a powerful modern method that allows for a complex and simultaneous cell analysis. This review is devoted to studies on atherosclerosis and CAD performed using flow cytometry.