In this chapter, we introduce modern magnetic resonance imaging (MRI)-based mouse brain atlases. Although unable to match the resolution and specificity of their histology-based counterparts, MRI-based mouse brain atlases feature higher anatomical fidelity and can facilitate high-throughput computer-assisted analysis of certain brain phenotypes. This chapter discusses several technical aspects of MRI-based mouse brain atlases, which are important to understand the usefulness as well as limitations of existing atlases. We focus on a novel MRI technique, diffusion tensor imaging (DTI), which provides rich tissue contrasts and is uniquely suited for studying white matter structures and immature mouse brains. The chapter then demonstrates several applications of MRI-based mouse brain atlases in anatomical phenotyping and guiding stereotaxic operations.