Many types of mammalian cells, such as sperm, blood, embryos, etc., have been successfully cryopreserved for the last few decades, while no optimal method for the cryopreservation of mammalian tissues or organs has been established, showing a poor survival after thawing with a low recovery of function. In this study, the freezing rate was determined by indirect thermodynamic calculation, and its potential effect on the cryoprotection of human saphenous veins and tissue-engineered bones was investigated. The vein segments were frozen according to the calculated freezing rate, using rate-controlled freezing devices, with a freezing solution composed of 10% dimethylsulphoxide and 20% fetal bovine serum in RPMI 1640 media. The efficacy of indirect calculation was assessed by the cell viability measured using fluorescence double-staining methods. The results indicated that the freezing rate determined by indirect calculation significantly (P < 0.05) maintained the post-thaw cellular viability of the blood vessel, particularly in terms of the endothelial cells. However, it exerted relatively less protective effect on the osteoblastic cell-cultured scaffolds. These results suggest that freezing-induced injuries may occur in tissues, and the freezing rate determined by indirect thermophysical calculation can be used for the optimization of tissue cryopreservation by minimizing the injuries.