Micro-computed tomography (micro-CT) is an essential tool for phenotyping and for elucidating diseases and their therapies for rodents in preclinical studies.  The strengths of micro-CT lie in its high resolution, relatively low cost, and scanning efficiency. Micro-CT provides a reliable platform for small animal imaging that is complementary to other small animal imaging methods, enabling numerous morphological and functional imaging applications. Micro-CT provides high-resolution anatomic information, either on its own or in conjunction with lower-resolution functional imaging modalities such as positron emission tomography (PET), single-photon emission computed tomography (SPECT), and optical imaging devices.  However, advanced applications of micro-CT produce functional information by translating clinical applications to model systems and by pioneering new ones.  The radiation dose and low contrast associated with x-ray imaging are well-known; however, newly developed contrast agents and novel acquisition and reconstruction strategies show extraordinary promise in overcoming these limitations.  Several image reconstruction strategies based on iterative, statistical, and gradient sparsity regularization are achievable with low radiation dose and more powerful computational resources.  In addition, two contrast mechanisms have also been developing to achieve these goals.  The first is spectral contrast for quantitative material discrimination in combination with passive or actively targeted nanoparticle contrast agents.  The second is phase contrast which measures refraction in biological tissues for improved contrast and potentially reduced radiation dose relative to standard absorption imaging.  Combined with exciting new opportunities in spectral and phase contrast imaging, these developments will surely continue to expand the applications for micro-CT in small animal models.  X-ray fluorescence computed tomography (XFCT) has been recently studied as a method for 3D imaging of low concentrations of probes containing high atomic number (Z) elements, showing promising results in detecting low concentrations of iodine, gadolinium, gold nanoparticles, and Cisplatin.  XFCT may expand the applications of CT in drug development.   These technological advancements promise to develop micro-CT into a more powerful, functional and even molecular imaging modality for preclinical studies.