Gene therapy of cancer has been one of the most exciting and elusive areas of scientific and clinical research in the past decade. One of the most critical issues for ensuring success of this therapy is the development of technology for noninvasive monitoring of the location, magnitude and duration of vector-mediated gene expression, as well as the distribution and targeting of vector particles in vivo. In recent years many advances have been made in high-resolution, in vivo imaging methods, including: radionuclide imaging, such as positron emission tomography (PET) and single photon emission tomography (SPECT), magnetic resonance (MR) imaging and spectroscopy, bioluminescence imaging and various fluorescence imaging techniques, including fluorescence-mediated tomography (FMT) and near-infrared fluorescence (NIRF) reflectance imaging. A variety of factors determine the choice of specific imaging system, some of them are the imaging requirements (single or repeated), intended use (animal or human) and spatial requirements (organs versus cellular resolution and depth). This review provides descriptions of modalities applicable to imaging different parameters of vector-mediated gene expression in tumors and stem cell tracking in vivo.