It is essential to visualize the structures of embryos and their internal organs three-dimensionally to analyze morphogenesis; this used to rely solely on serial histological sectioning and solid reconstruction, which were tedious and time-consuming. We have applied imaging with a magnetic resonance (MR) microscope equipped with a 2.35 T superconducting magnet to visualize human embryos; we were successful in acquiring high-resolution sectional images and in identifying the detailed structures of major organs. The imaging process was facilitated by using a super-parallel MR microscope. A dataset of MR images of more than 1,000 human embryos, now collected, will be important for future biomedical research and for education.