Molecular imaging with contrast ultrasound relies on the detection of targeted microbubbles or other acoustically active nanoparticles. These microbubbles are retained in diseased tissue where they produce an acoustic signal because of their resonant properties in the ultrasound field. Targeting is accomplished either through manipulating the chemical properties of the microbubble shell or through conjugation of disease-specific ligands for the targeted molecule to the microbubble surface. As microbubbles cannot leave the intravascular space, the disease process must be characterized by molecular changes in the vascular compartment to be imaged. Inflammation, angiogenesis and thrombus formation are central pathophysiologic processes in many disease states and produce phenotypic changes in the vascular compartment. Thus, targeted contrast ultrasound in the future could aid in the diagnosis of such diverse diseases as atherosclerosis, transplant rejection and tumor-related angiogenesis.