Magnetic resonance (MR) microscopy was used to noninvasively investigate the development of live rat embryos in utero. The difficulty in making sequential observations of a developing mammalian embryo has frustrated developmental biologists for many years. Most current technologies analyze normal and abnormal development by observing end point phenotypes (in fixed specimens) rather than investigating the live embryo. MR microscopy was adapted to allow rat litters to be scanned three times each (at 1- to 3-day intervals) and has produced images of live developing embryos. It was demonstrated that repeated anesthesia and imaging protocols produced no gross malformations in the rat pups that were subsequently delivered and observed. Three-dimensional projection encoding with phase rewinders produced isotropic (256(3)) image data sets in about 30 minutes with excellent tissue contrast arising from steady-state effects in the amniotic fluid.