Imaging has the ability to study various biological and chemical processes noninvasively in living subjects in a longitudinal way. For this reason, imaging technologies have become an integral part of the drug-discovery and development program and are commonly used in following disease processes and drug action in both preclinical and clinical stages. As the domain of imaging sciences transitions from anatomical/functional to molecular applications, the development of molecular probes becomes crucial for the advancement of the field. This review summarizes the role of two complementary techniques, magnetic resonance and fluorescence optical imaging, in drug discovery. While the first approach exploits intrinsic tissue characteristics as the source of image contrast, the second necessitates the use of appropriate probes for signal generation. The anatomical, functional, metabolic and molecular information that becomes accessible through imaging can provide invaluable insights into disease mechanisms and mechanisms of drug action.