Abstarct: Pod distortion syndrome (PDS) is a special type of growth that soybeans remain green during long time after pods maturity. This syndrome can produce many problems at harvest time and it can reduce the plant performance. In this research, the comparison of the protein exxpression profiles of healthy and infected plants was performed in order to investigation of soybean podding abnormality reasons in Katul cultivar. For this purpose, root samples were selected at R6 vegetative stage via roving method and their protein was extracted by phosphate buffer extraction method. Two-dimensional electrophoresis gel resulted in the appearance of 124 repeatable protein spots. The 34 spots were significantly altered in protein exxpression baxsed on IF index (induction factor). By performing t-test, 11 protein spots were significant at 5% probability level. Most of these proteins were involved in energy production, mextabolism, signal transduction, protein splitting and storage. Glutamate dehydrogenase, melatonin, glycoprotein 31 kDa stem, 14-3-3-like protein, as well as Ros proteins and detoxification including Germin like protein and Thioredoxin, and an unknown protein, showed a reduction of exxpression in response to this problem. In general, these results indicate that changes in the exxpression of certain proteins in the root of plants may in turn play a significant role in the appearance of soybean podding abnormality.