Objective To analyze the serum proteome change after liver transplantation and FK506 combination in human serum by two-dimensional gel electrophoresis (2-DE) and to study the mechanism of immune rejection and the mechanism of action of FK506 combination. Methods The serum samples of 5 liver transplantation patients pre- and post transplantation at 24 hours,10 days,30 days,90 days 180 days were treated using Aurum Serum Protein Mini Kit, and than analyzed by 2-DE. The electrophoresis images were analyzed by using ImageMaster 2D platirum imaging analysis software. Results The differential maps of 2-DE of serum proteome before and after liver transplantation and FK506 combination were established. Protein spots between (877?59.65)-(897.6?61.01),the matching rate before transplantation and different groups after transplantation>70%. Among them 7 protein spots were selected with good repeatability and significant differential expression. Conclusions The 2-DE analytical method of serum proteome after liver transplantation and FK506 combination was preliminarily established. The differential expression protein spots found in the study have laid a foundation for the further study .