Objective To improve the method of paraffin section preparation of whole mouse embryos and newborn mice. Method Specimens of mouse embryos and newborn mice were collected. Embryos aged 14.5, 15.5 and 16.5 days were directly placed in 4% neutral formaldehyde and fixed for more than 24 hours. For embryos aged 17.5 and 18.5 days, and 0-, 1- and 2-day old newborn mice, a small amount of formaldehyde was slowly injected into the chest, abdomen and brain at first, respectively, and then the whole specimens were fixed for more than 24 hours. Tissues were processed together using a fully-enclosed tissue processor. Paraffin-embedded slices were observed under microscope after HE staining. Results The quality of specimens following the improved method was better than before. The structure of different tissues from both mouse embryos and newborn mice can be easily determined. No fragmentation was found in any organ tissue under the light microscope. Conclusions We can handle whole body specimens of both mouse embryos and newborn mice simultaneously by adjusting the program of the fully-enclosed tissue processor. The staining results of the sections which were dehydrated using this improved method are clear and stable. This improved method may provide a useful approach in research of genetics and developmental biology.