AIM:To test the difference of protein composition in tear between cornea transplantation immunological rejection rats and rats with no rejection by SELDI protein chip technology, and to find cornea transplantation immunological rejection associated protein and deduce the possible mechanisms of cornea transplantation immunological rejection.METHODS: To build homogeneity penetrability corneal transplantation rat model: The grafts of group Ⅰ came from side-center and the suture tail remained about 1mm while grafts of group Ⅱ came from center cornea and the suture remained as short as possible. Slit-lamp microscopy was used to observe the three indexes of cornea score in opacity, edema and new vessels from the 1^st day after operation. The result data were as mean±SD and tested by independent-sample ttest in SPSS 13.0 software. The difference was set at P＜0.05. The tears were collected at the 7^th. Capture marker with WCX2 protein chip. Then find out the protein combination that can best distinguish the two group samples. Preliminary screening the marked proteins in Swiss-Prot and TrEMBL protein library.RESULTS: The 7^th day post-operation was sample collection time. It is the time to distinguish the graft rejection group from non-rejection group. 108 proteins were marked in total in two groups, there are 11 kinds of proteins with classified value, among these 6 kinds got high classify value. The result of albumin search library result suggested that the related albumin maybe Neuropeptide Y, β-defensin 1,Glucagon,and Cortistatin-14.CONCLUSION:It is reliable to obtain proteomic profiles in tear for rat marker of cornea graft rejection using SELDI-TOF-MS with well reproducibility. The results suggest that neuripeptide and energy maybe play an important role in graft rejection.