There is growing interest in the availability of methods for imaging disease at the level of the cellular and/or molecular mediators. Techniques for imaging molecular alterations have been develop for essentially all non-invasive cardiac imaging modalities. Molecular imaging with contrast-enhanced ultrasound relies on the detection of novel site-targeted contrast agents. These microbubbles or nanoparticles are retained within regions of a specific disease process, thereby allowing phenotypic characterization of tissue. Since most of these tracers remain within the intravascular space, the disease processes assessed must be characterized by antigens that are expressed within the vascular compartment. Accordingly, the pathologic states that have been targeted include inflammation, ischemia-and tumor-related angiogenesis, and thrombus formation; all of which are mediated in part by molecular events within the vascular space. This review describes: 10 different strategies that have been employed to target ultrasound contrast agents to regions of disease, 2) the unique challenges for imaging targeted ultrasound contrast agents, and 3) some of the early experience imaging molecular events in animal models of disease.