The atomic structure of multi-wall carbon nanotubes (MWCNTs) implanted in the subcutaneous tissue of rats was examined by means of high-resolution transmission electron microscopy (HRTEM). Clusters of the MWCNTs implanted in the subcutaneous tissue were well recognized by the TEM observations. It was indicated that some nanotubes were taken in phagocytes after the 1-year implantation. The deterioration of crystalline structure of the nanotubes in phagocytes was shown by the HRTEM observation. It was suggested that the deterioration of the nanotubes was due to the peeling of the outer graphene layers in the phagocytes.