To conduct a systematic study of the immunologic response of rats to transplanted glutaraldehyde (GA)-treated porcine blood vessels in vivo using proteomics. The experiment was divided into two groups: a fresh group and a glutaraldehyde-treated group. Twenty fresh and glutaraldehyde-treated porcine pulmonary arteries were subcutaneously embedded in rats. We compared the changes using immunohistochemistry and enzyme-linked immuno sorbent assay (ELISA). Proteomic analysis via a label-free shotgun strategy was performed. As measured by immunohistochemistry, CD4, CD8 were more strongly expressed on day 12 and day 30 in the fresh group. Their expression levels in the glutaraldehyde group were weaker than or similar to those in the fresh group. From ELISA, the expression levels of IL-6 followed a similar pattern, but IL-2 level reached a peak on day 4. From proteomic analysis, a total of 1278 proteins in fresh group and 1064 proteins in glutaraldehyde-treated group were identified, 280 proteins were up-regulated, and 237 proteins were down-regulated. These altered proteins belonged to three broad functional categories: metabolic, cytoskeletal and stress response. Six proteins to have significant differences in their expression are associated with apoptosis and the immune/inflammatory response. Glutaraldehyde-treated xenogenic blood vessels elicited an immune response, albeit lower than that of fresh blood vessels. The proteomics shotgun strategy used in this study can separate and analyze immunological proteins effectively, which improved the immunological protein expression profiles of fresh and glutaraldehyde-treated groups. The six proteins identified may serve to further explore the immunological response mechanisms.