Molecular imaging with targeted contrast agents by magnetic resonance imaging (MRI) allows for the noninvasive detection and characterization of biological changes on a molecular level. In this article, the principles of molecular MRI and its applications in cardiovascular diseases are reviewed. First, basic properties of positive and negative contrast agents are introduced and their effect on signal generation in a magnetic field is described. In the next part, different types of MRI scanners and the influence of field strength on signal properties of contrast agents for molecular imaging are discussed. Additionally, the assessment, analysis, and quantification of the changes in T1 and T2* relaxation time induced by the different molecular contrast agents are reviewed. Finally, the basic mechanisms of targeting of imaging probes on a molecular level and recent applications of molecular MRI in cardiovascular disease are reviewed.