Gastrointestinal digestibility of new proteins inserted in food supply is one of significant parameters for assessing safety of genetically modified (GM) foods on the assumption that digestive stability is undesirable. Digestive stability of GM soybean was evaluated under the physiologically based in vitro digestion model. Electrophoresis was used to follow the in vitro sequential digestions/fermentation procedure and Western blotting was employed to confirm the new protein in GM soybean. CP4EPSPS newly expressed in GM soybean was completely digested in 15 s in the gastric fluid in this model. In the assay of fermentation of new protein, CP4EPSPS was also complete degraded and no fermentation products were found during 24 h of colon fermentation. Results from this study suggested that CP4EPSPS in GM soybean does not have a potential allergenicity due to its complete digestion within a very short time in gastric fluid. No formation of colonic protein fermentation products confirms that new protein is not capable of initiating colon cancer.