Several techniques for structural and functional tomographic imaging are utilized in the molecular imaging research field to characterize animal models. Preclinical imaging has emerged as an important non-invasive tool to facilitate anatomical and functional phenotyping in small rodents for studying normal pattern and models of human disease. Modern biomedical research is rapidly evolving to include sophisticated imaging analysis like high resolution X-ray based techniques, nuclear imaging technologies, ultrasound biomicroscopy or magnetic resonance. Over the last years these modalities have been improved to address the needs of researchers to analyse living animals in longitudinal studies. Moreover, the phenotyping strategies of murine models through imaging aim to promote multidisciplinary translational research by assisting in the characterization of genetically modified animal models of human diseases. We showed that morpho-functional imaging methods have strengthened the options of in vivo visualization of cancer-related processes over time, evaluation of metabolism, body composition and bone mineral density, cardiovascular phenotyping and neurological studies in mouse models.