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Our previous study showed that a cryopreserved tracheal allograft could be transplanted using omentopexy without immunosuppression. The present study investigated, by the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method, whether the regenerated epithelia were of recipient origin or donor origin in a cryopreserved tracheal allotransplantation model.Twenty-nine mongrel dogs were classified by preoperative peripheral blood PCR-RFLP analysis. The cryopreserved tracheal allografts were implanted into recipient animals that showed a different phenotype from donor animals. A small specimen of epithelia excised from the allograft of animals postmortem was analyzed with the modified PCR-RFLP method.The animals were separated into 16 phenotypes by preoperative PCR-RFLP results, and cryopreserved tracheal allografts transplanted into 8 animals. PCR-RFLP analysis of graft epithelia at 10 days after transplantation showed the donor blood phenotype and analysis of graft epithelia taken from the animals that survived more than 20 days after operation showed the recipient blood and epithelial phenotype.The donor epithelia in the grafts were no longer present within about 20 days after transplantation. The recipient epithelia migrated gradually from the anastomotic site, and the regenerated epithelia that are of recipient origin covered the allograft within about 50 days after transplantation.