Three-dimensional observation during embryogenesis is possible with micro-computed tomography, but there are no observations of organ size. In this paper, three examples of three-dimensional observation of organs by micro-CT are tried. At 13.0 days post-coitum, mouse embryos were fixed in 4% paraformaldehyde for 24 h and stained enbloc by osmium tetroxide overnight. The embryos were then embedded in paraffin using standard methods for 24 h. Specimens were analyzed by micro-computed tomography and image processing was performed. The entire Meckel's cartilage and its relation in the mandible, as well as the complex structure of the otocyst, are easily visualized. Although it is difficult to extract detailed structures of the tongue muscles, it is possible to identify the inner and external tongue muscles. Relation among the organs and other are easily visualized. Three-dimensional observation by micro-computed tomography is an important technology for visualization of embryogenesis and could be used in organ culture.