We evaluated the efficiency of several protocols to preserve the main components of decellularized tissue scaffolds for delayed use. Decellularized rat intestine scaffolds were generated by using SDS and triton X-100 and preserved for 3 months subjected to eight freeze-drying (F1 to F8) and 14 cryopreservation protocols (C1 to C14). Morphological analysis showed that cryopreservation tended to preserve the tissue morphostructure more efficiently than freeze-drying. Histological analysis showed that the content of proteoglycans and glycoproteins was efficiently preserved by most methods. The protocols that most efficiently preserved collagen fibers were those using trehalose and saccharose for freeze-drying (F2, F3, and F7 protocols) and DMSO, albumin, and saccharose (C3, C5, C6, C12) for cryopreservation. Most freeze-drying protocols and cryopreservation protocols with DMSO, albumin, and maltose (C6, C7, C13, and C14) efficiently preserved reticular fibers. For the elastic fibers, freeze-drying methods with trehalose and maltose (F2, F4, F6, and F8) properly preserved these fibers, with the results of most cryopreservation methods comparable to controls. These results suggest that freeze-drying using 0.1M trehalose and cryopreservation in the presence of 8% DMSO and 4.6% albumin are more efficient than other protocols in preserving the scaffold morphostructure and histological composition. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 488-500, 2018.