Extensive genetic information and the expanding number of techniques available to manipulate the genome of the mouse have led to its widespread use in studies of brain development and to model human neurodevelopmental diseases. We are developing a combination of ultrasound and magnetic resonance micro-imaging approaches with sufficient resolution and sensitivity to provide noninvasive structural, functional and molecular data on developmental and disease processes in normal and genetically-engineered mice. Our efforts over the past decade have focused on in utero and early postnatal imaging and analysis of the developing brain and cerebral vasculature. The advantages and limitations of both ultrasound and MRI for imaging mouse development will be discussed, and examples provided to illustrate the utility of these approaches for 4D mutant phenotype analysis. Recent advances have also made in the area of molecular imaging, including the generation of novel reporter mice that enable cell-specific imaging with ultrasound and MRI contrast agents. Future directions for molecular imaging of mouse brain development will be discussed.