Use of transponders, small electronic identification devices, in experimental swine is expected to be more reliable than the current common use of ear tags. However, it is necessary to determine the optimal implantation site for transponders with high readability, retentionability (i.e., long-term retention in tissues without detachment or loss), and biocompatibility, as this has not yet been investigated. Thus, we aimed to determine the optimal implantation site. Two types of transponders were subcutaneously implanted into four different sites (ear base, ear auricle, ventral neck, and back) in 3 domestic swine each. The transponders were scanned at 1, 2, 3, and 84 days after implantation. The location of the transponders was examined by X-ray and echography at 84 days. Histopathological examinations were performed at 84 days. The transponders in the back were successfully scanned in a shorter time than those in other implantation sites, without any re-scanning procedures. X-ray examination revealed one transponder in the ventral neck was lost, whereas those in the other sites were retained in their original location for 84 days. Echography indicated that the transponders in the back were retained more deeply than those in other implantation sites, suggesting better retentionability. Acceptable biocompatibility was confirmed in all implantation sites, as evidenced by the finding that all transponders were covered by a connective tissue capsule without severe inflammation. In conclusion, the present results demonstrated that the back is the optimal implantation site for transponders in experimental swine.