The 3D internal structure microscopy (3D-ISM) was applied to the equine ovary, which possesses peculiar structural characteristics. Stereolithography was applied to make a life-sized model by means of data obtained from 3D-ISM. Images from serially sliced surfaces contributed to a successful 3D reconstruction of the equine ovary. Photopolymerized resin models of equine ovaries produced by stereolithography can clearly show the internal structure and spatial localizations in the ovary. The understanding of the spatial relationship between the ovulation fossa and follicles and/or corpora lutea in the equine ovary was a great benefit. The peculiar structure of the equine ovary could be thoroughly observed and understood through this model.