Molecular MRI plays an important role in studying molecular and cellular processes associated with heart disease. Targeted probes that recognize important biomarkers of atherosclerosis, apoptosis, necrosis, angiogenesis, thrombosis and inflammation have been developed. This review discusses the properties of chemically different contrast agents including iron oxide nanoparticles, gadolinium-based nanoparticles or micelles, discrete peptide conjugates and activatable probes. Numerous examples of contrast agents based on these approaches have been used in preclinical MRI of cardiovascular diseases. Clinical applications are still under investigation for some selected agents with highly promising initial results. Molecular MRI shows great potential for the detection and characterization of a wide range of cardiovascular diseases, as well as for monitoring response to therapy.