Abstract: AIM To establish and to optimize the two-dimen-sional (2-D) polyacrylamide gel electrophoresis (PAGE) for investigating the different expression of colonic proteins in BALB/c mice induced by extract of senna, and to lay the foundation for screening and characterization of biological molecules mediating the effect of senna from the gastrointestinal tract. METHODS The model of chronic gastrointestinal motility hyperfunction in mice was established by intragastric administration of senna extraction. The proteins of colon was extracted from control and model mice. The 2-D PAGE was optimized for analyzing the different expression of proteins. The 2-D PAGE gels were stained with silver staining. RESULTS An animal model of chronic gastrointestinal motility hyperfunction was established in mice. Optimized 2-D PAGE displayed the different expressional proteins in gastrointestinal tract of model mice. CONCLUSION The different expression of colonic proteins can be induced by extract of senna in BALB/c mice. These proteins maybe mediate the effect of senna in gastrointestinal tract.