In order to develop an efficient method about protein extraction which is suitable for apple proteomic analysis, four protocols of total protein extraction from apple leaves, which are trichloroacetic acid/acetone precipitation method (TCA), phenol extraction methanol/ammonium acetate precipitation method, Tris-HCl extraction method and modified Tris-HCl extraction method were compared. The results showed that the modified Tris-HCl extraction method was the most suitable method in protein extraction for two-dimensional electrophoresis (2-DE) from apple leaves based on the highest resolution and more informative spots of2-DE gels with no apparent vertical or horizontal streaking.