In this study a combination of 3D multi gradient echo (MGE) and ultrashort echo time (UTE) 100 micron isotropic resolution where acquired from 6 fixed mouse embryos at embryonic day 16. The embryos where littermates from an engrailed knockout mouse whose mutant embryos die at birth. The data from the UTE was validated with a high resolution CT scan. Results verify the utility of this approach to image both soft tissue and the skeletal system in a high throughput manner. The expected phenotype was easily identifiable and the 3D reconstruction of the skeletal system was equivalent to CT.