The roots of Platycodon grandiflorum are known as traditional medicine, has been extensively used since ancient times as a therapeutic to treat cold, cough and asthma in Korean traditional medications. This study was conducted in order to profile proteins from the hormone induced diploid and tetraploid roots using high throughput proteome approach. Two dimensional gels stained with CBB, a total of 64 differential expressed proteins were identified from the diploid root using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 20 differential expressed protein spots (≥ 2-fold) were analyzed using MALDI-TOF-TOF mass spectrometry whereas a total of 13 protein spots were up regulated and 7 protein spots were down-regulated. However, in the case of tetraploid root, a total of 78 differential expressed proteins were identified from tetraploid root of which a total of 28 differential expressed protein spots (≥ 2-fold) were analyzed by mass spectrometry whereas a total of 16 protein spots were up regulated and a total of 12 protein spots were down-regulated. However, proteins identified using iProClass databases revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase activity, transporter activity and isomers activity. The exclusive protein profile may provide insight clues for better understanding the characteristics of proteins and metabolic activity in various explants of the economically important medicinal plant Platycodon grandiflorum.