Atherothrombosis and the resulting coronary heart disease and stroke, are the most common causes of death in developed countries. The molecular basis of the pathophysiology of atherothrombosis remains largely unknown. As a consequence, although cardiovascular medicine has been able to reduce the incidence of this disorder, it still fails to avoid the development of acute vascular events, such as stroke and acute coronary syndromes (ACS). In the last years, there has been an explosion in the search for novel biomarkers that may help the clinician to predict the probability of recurrence of atherothrombosis. The classical way to address the study of this disorder and the development of new biomarkers was to focus in one, two or a few candidate molecules. However, the arrival of new proteomic techniques into the field of cardiovascular research will allow analyzing the expression of multiple proteins at once. Using proteomic techniques, it is possible to study the proteome of cells involved in atherosclerosis with different approaches. We have analyzed the proteome of the supernatant of cultured atherosclerotic plaques and from circulating monocytes in subjects with an acute coronary syndrome. Other authors have also studied the proteome of cultured cells involved in this disorder. The results of these approaches are lists of proteins differently expressed in atherothrombosis. The involvement of these molecules in this disorder should be addressed in functional studies in vitro and in experimental models. Those proteins related to the pathophysiology of atherothrombosis also displaying stable plasma levels should be good candidates to be patented as potential biomarkers and tested in large populations.