Transplantation of the trachea may become the preferred method for the reconstruction of extensive tracheal defects, however, several unresolved problems must be addressed, such as immunosuppression, preservation and donor shortage. In this manuscript, the cryopreservation of tracheal grafts is reviewed, which potentially is associated with a lessened immunological response. Cryopreservation may be used clinically for long-term preservation and may solve the donor shortage. It is very important to confirm the immunomodulatory effect of cryopreservation on tracheal allografts in order to expand the potential clinical application of tracheal transplantation in the future. The cartilage as well as the epithelium and lamina propria serve as targets for rejection. However, the effect of cryopreservation on chondrocytes could be associated with reduced allogenicity of the trachea. The long-term cryopreservation of cartilage must be investigated in basic research models of chondrocyte viability. Growth of cryopreserved tracheal allografts is less well understood. Further studies are needed to elucidate the mechanism of synergistic effects of both cryopreservation and adequate immunosuppression for tracheal xenografts.