The practice of clinical cardiology employs many imaging techniques for diagnosis, risk stratification and therapeutic monitoring. These imaging modalities largely provide anatomical or structural information, and only indirectly reflect underlying molecular events. Molecular imaging techniques report on entities or processes that can be defined at the molecular, as opposed to the anatomical, level. For example, molecular imaging can reveal the expression or activity of a specific protein, the fate or localization of a biomolecule, or the activity of a biological pathway. This Review highlights key processes and molecular targets that are currently being investigated experimentally by molecular imaging probes in vivo. Collectively, these targets have an important role in the development of atherosclerosis and acute plaque rupture, as well as in myocardial disease. Molecular imaging technology is now progressing towards clinical application in humans and has the potential to guide diagnosis, risk assessment and treatment response. Imaging-based surrogate end points could speed the development of new drugs, particularly those with novel mechanisms of action. More broadly, by noninvasively reporting on molecular processes in vivo, molecular imaging can reveal how specific proteins or pathways function in their native context, thus contributing to a systems-level understanding of cardiovascular disease biology.