Molecular imaging aims towards the non-invasive kinetic and quantitative assessment and localization of biological processes of normal and diseased cells in vivo in animal models and humans. Due to technological advances during the past years, imaging of molecular processes is a rapidly growing field, which has the potential of broad applications in the study of cell biology, biochemistry, gene/protein function and regulation, signal transduction, characterization of transgenic animals, development of new treatment strategies (gene or cell-based) and their successful implementation into clinical application. Most importantly, the possibility to study these parameters in the same subject repeatedly over time makes molecular imaging an attractive technology to obtain reliable data and to safe recourse; for example, molecular imaging enables the assessment of an exogenously introduced therapeutic gene and the related alterations of endogenously regulated gene functions directly in the same subject. Therefore, molecular imaging will have great implications especially when molecular diagnostic and treatment modalities have to be translated from experimental into clinical application. Here, we review the three main imaging technologies, which have been developed for studying molecular processes in vivo, the disease models, which have been studied so far, and the potential future applications.