Small animal positron emission tomography (PET) and computer tomography (CT) is an emerging field in pre-clinical imaging. High quality, state-of-the-art instruments are required for full optimization of the translational value of the small animal studies with PET and CT. However, with this achieved the possibilities are numerous and the role of pre-clinical imaging crucial for a prompt movement from bench to bedside. Several new tracers are under preclinical and clinical evaluation and most are directed at central aspects of tumor biology. We hereby present some of the recent advances in this field of small animal molecular imaging with special emphasis on the targets for tissue characterization in tumor biology such as hypoxia, proliferation and cancer specific over-expression of receptors. The added value of applying CT imaging for anatomical localization and tumor volume measurements is also described. In addition, the non-invasive nature of molecular imaging and the targets of these promising new tracers are attractive for other research areas as well, although these fields are much less explored. We present an example of an interesting research field with the application of small animal PET/CT for studies of muscle and tendon in exercise models. © 2011 Bentham Science Publishers Ltd.