The three-dimensional structure of scabies mites (Sarcoptes scabiei var. hominis) and keratin layers affected by crusted scabies lesions were obtained using X-ray computed tomography at sub-micrometer and micrometer resolution, respectively (X-ray micro-CT). Clear three-dimensional images including internal structure of scabies mites were obtained. Utilizing reconstructed micro-CT data, the sections of the capitulum (head part), digestive organs, and legs are shown. The reconstructed capitulum shows a jaw-like structure capable of penetrating the keratin layer of the skin. The tip of the forelegs of female scabies mites has a flat disk structure that may be used to grasp the skin surface. The keratin layer of a crusted scabies lesion spontaneously exfoliated from a patient was also reconstructed by the X-ray micro-CT technique. Extracted sections from CT data revealed a network structure of tunnels made by scabies mites with numerous larvae and eggs inside the tunnels.