Magnetic resonance histology (MRH) has found considerable application in structural phenotyping in the mouse embryo. MRH employs the same fundamental principles as clinical MRI, albeit with spatial resolution up to six orders of magnitude higher than that in clinical studies. Critical to obtaining this enormous gain in resolution is the need to enhance the weak signal from these microscopic voxels. This has been accomplished through the use of active staining, a method to simultaneously fix the embryonic/fetal tissues, while reducing the spin lattice relaxation time (T1). We describe here the methods that allow one to balance the fixation, which reduces the nuclear magnetic resonance (NMR) signal, with the enhancement of signal derived from the reduction in T1. Methods are included to cover the ranges of embryonic specimens from E10.5 through E19.5.