Ultrasound biomicroscopy (UBM) and magnetic resonance microimaging (micro-MRI) provide noninvasive, high-resolution images in mouse embryos and neonates, enabling volumetric and functional analyses of phenotypes, including longitudinal imaging of individual mice over critical stages of in utero and early-postnatal development. In this chapter, we describe the underlying principles of UBM and micro-MRI, including the advantages and limitations of these approaches for studies of mouse development, and providing a number of examples to illustrate their use. To date, most imaging studies have focused on the developing nervous and cardiovascular systems, which are also reflected in the examples shown in this chapter, but we also discuss the future application of these methods to other organ systems.