In order to clarify the complete cytomorphology of cytopathic changes as a consequence of human papillomavirus (HPV) infection, we performed three-dimensional (3D) reconstruction from confocal fluorescent images. After confirming 22 HPV types using a DNA chip, we performed 3D confocal image restoration in human uterine cervical swab samples and corresponding tumor tissues. On restoration of 3D confocal images, the multinucleated feature of koilocytes was revealed to be multilobation of a single nucleus, as opposed to true multinucleation.