Using 4 and 8-channel super-parallel magnetic resonance (MR) microscopes with a horizontal bore 2.34T superconducting magnet developed for 3-dimensional MR microscopy of the large Kyoto Collection of Human Embryos, we acquired T1-weighted 3D images of 1204 embryos at a spatial resolution of (40 μm)3 to (150 μm)3 in about 2 years. Similarity of image contrast between the T1-weighted images and stained anatomical sections indicated that T1-weighted 3D images could be used for an anatomical 3D image database for human embryology.