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.