Soy and fermented soy are popular and recognized as a health food among Koreans. Since soy proteins are known to be protease resistant, even to pepsin and pancreatin, it is hypothesized that soy proteins may interact with the intestinal tract and trigger certain physiological reactions. To test this hypothesis, mice were fed diets supplemented with soy, Chunkukjang, or casein. The differentially expressed proteins were analyzed using 2-D gels and identified by peptide mass fingerprinting using mass spectrometry. The majority of the differentially expressed proteins could be functionally grouped into metabolic enzymes and calcium-binding proteins. The differential protein expression by the soy-fed groups was also verified based on a representative protein, tropomyosin, using a Western blotting analysis. In addition, the soy-fed groups exhibited a taller villi structure. Therefore, this study suggests that soy proteins can be an effective nutrient and physiological stimulant for the intestines.