Little is known on the outcome of tracheal allografts after long-term survival. This study aimed to explore the changes in structure and composition by evaluating the status of the mucosa and cartilage of allografts with long-term survival in dogs. Eight tracheal allografts that survived for ˃9 months were enrolled in our study. Epithelium, revascularization, monocyte infiltration and fibrosis were evaluated histologically. The fluorescent dye 4'-6-diamidino-2-phenylindole was used to evaluate the presence of chondrocyte nuclei. Glycosaminoglycan was detected using safranin-O staining and collagen II was evaluated using immunohistochemistry. The 8 animals survived from 277 to 783 days. Bronchoscopy demonstrated that 6 allografts showed no stenosis; 2 cases developed slight stenosis, but could maintain airway patency. Histological examination showed that the epithelium covered the surface of the allografts. In comparison to fresh tracheal controls, allografts demonstrated mild monocyte infiltration, evident revascularization and mild fibrosis in the mucosa or submucosa (all P < 0.05). There were a few viable chondrocytes scattered in the cartilage after long-term survival. Moreover, glycosaminoglycan and collagen II were significantly decreased in the allografts compared with fresh trachea (all P < 0.05). For tracheal allografts with long-term survival after transplantation, only a few viable chondrocytes were retained, and the extracellular matrix of the cartilage demonstrated degeneration. Despite this, the airway could maintain patency. Notably, the significance of monocyte infiltration in the mucosa or submucosa at different time points warrants further study.