Molecular imaging, including reporter gene methods, provides a unique opportunity to study biology in a living subject, thereby allowing physiological events to be monitored in an intact microenvironment. This review takes a molecular and cell biology perspective on recent studies which utilize reporter gene imaging as a tool to non-invasively monitor specific molecular biology pathways in vivo. Studies in rodent models demonstrate the feasibility of reporter gene imaging to visualize and measure key cellular pathways, such as transcription, translation and protein-protein interactions. The review indicates that molecular imaging is likely to be useful in the translation of molecular biology to medicine and biotechnological applications.