Despite enormous therapeutic advances, coronary artery disease (CAD) remains a global public health problem. Effective prevention of cardiovascular morbidity and mortality will require the development of new diagnostic and therapeutic strategies aimed at treating early, subclinical disease stages. These novel approaches are increasingly based on the molecular understanding of disease development. Molecular imaging, as it applies to CAD, describes diagnostic strategies targeting biomarkers associated with the development of atherosclerotic lesions. In analogy to applications in oncology, identification of subclinical disease and disease activity appear feasible. Novel therapeutic strategies include the development of targeted transport vehicles allowing drug delivery to specific cells or cell structures. Nanotechnology is expected to contribute to molecular strategies in the diagnosis and treatment of CAD. Of particular interest are bioengineered nanoparticles, which can be utilized as transport vehicles of diagnostic or therapeutic agents. However, further development is required before nanotechnology can be applied clinically. This manuscript also includes some recent patents on this topic.