The differences of physiological characteristics between Bt-cotton and non-Bt cotton were determined in this study.The seedlings of 4 varieties,Lumianyan 17,DGL 99102,Zhongmiansuo 12 and Xinmian 33B,were used to investigate the activities of POD and SOD,the contents of protein,amino acid,MDA and photosynthetic pigment.The results showed that the activities of POD,SOD,contents of protein and amino acid in Bt-cotton were significantly higher than those in non-Bt cotton,while it got the opposite effect in the content of MDA.Therefore,the capability of eliminating free radical of active oxygen of Bt-cotton was better than that of the non-Bt cotton.However,the diversity of photosynthetic pigment content had no regular pattern.The capability of osmoregulatory of the Bt-cotton was higher than that of non-Bt cotton.