The present investigation was aimed to detect the specific protein polypeptide(s) appeared during the organogenesis stages of differentiation in Solanum trilobatum L. Among different explants, only internode showed good results for micropropagation. To analyze and compare their variation of protein profiles were assessed from callus, organogenic calls, multiple shoots, root, and regenerated plants. The highest response of callus induction (92.8%) was observed in 2.5 mg/l of 2,4-D (2, 4-dichlorophenoxyacetic acid) supplemented in Murashige and Skoog’s (MS) medium. Organaogenic callus induction was maximum (34.6%) in medium supplemented with 2,4-D 3.0 mg/l. α-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) and 2,4-D with BAP various combinations were showed variable redifferentiation response along with callus formation and multiple shoot initiation. The medium supplemented with 3.0 mg/l BAP with 3.0 mg /l of 2,4-D showed better shoot multiplication (87.6%) and elongation. High rate of root induction (68.3%) was observed on medium supplemented with NAA (1.0 mg/l). Simultaneous induction of shoot and root (58.4%) was observed in MS medium supplemented with BAP 2.0 mg/l with NAA 1.0 mg/l. For best plantlet regeneration was achieved in (86.2%) medium supplemented with BAP 2.0 mg/l with NAA 1.0 mg/l. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed a unique protein bands in tissues. Significantly different pattern and concentration of total soluble proteins were seen in differentiation of callus to plantlet regeneration stages. Polypeptide banding pattern of regenerated plants were different from naturally growing plants. When comparing the protein bands in cultures of each stage they were different to each other. The molecular weights of detected bands for all samples ranged from 62.66 to 86.51 KDa. Three similar culture specific callus, Organogenic callus and root polypeptides (MW 86.65, 83.45 and 80.10 kDa) and four shoot specific polypeptides (MW 86.51, 83.25, 80.18, and 62.66 kDa) and were synthesized during the differentiation. Similarly, one shoot specific (MW 62.66 kDa) and two regenerated plants specific (MW 77.52 and 75.32 kDa) polypeptide band were appeared during differentiation in S. trilobatum. In vitro regenerated plant cultures showed totally five (MW 86.34, 83.78, 80.44, 77.52 and 75.32 kDa) plant specific polypeptides.