Magnetic resonance imaging (MRI) is increasingly becoming an important tool to study anatomy of rodent brains. Compared with histology, it has clear advantages because the entire 3D object can be captured as an image nondestructively. However, low imaging resolution and a small number of available contrast mechanisms are two critical disadvantages. In this article, the future potential of magnetic resonance (MR) microimaging is discussed, with special emphasis on diffusion tensor microimaging as an effective contrast mechanism for the developing central nervous system.