Feasibility of magnetic resonance imaging (MRI) and ultrasound biomicroscopy (UBM) for sequential in vivo study of mouse embryo development between Days 6.5 and 13.5 of pregnancy was assessed in a first experiment. A second trial, based on the results of the first, determined the accuracy of UBM for imaging morphogenesis from implantation to the late embryo stage (Days 4.5 to 15.5). MRI allowed imaging of the entire uterus and all gestational sacs and embryos inside whilst the small scanning range of UBM precluded accurate counting of fetuses; however, its high resolution identified the decidual reaction at implantation sites from Day 4.5. At later stages, it was possible to assess key morphogenetic processes such as differentiation of the placenta, the cephalic region, the thoracic and abdominal organs, the skeletal system and the limbs, and dynamic structures such as the cardiovascular system. Thus, both techniques are reliable for in utero imaging of mouse embryo development. MRI may be more appropriate for studying embryo lethality and intrauterine growth retardation, because the entire uterus can be viewed. UBM may be more suitable for studies of cellular components of organs and tissues and assessment of haemodynamic changes in the circulatory system.