Background: The diagnostic differentiation between Crohn's disease (CD) and ulcerative colitis (UC) is sometimes difficult. To date, there Lire no serological markers that are specific and sensitive enough to differentiate between these 2 diseases. Early and sal. e prediction of the inflammatory bowel disease (IBD) type is of great importance for the specific treatment of IBD patients. We thus analyzed and compared the expression of catalytic proteasome subunits in the out of mice and in the normal and inflamed intestines of CD and UC patients and assessed whether the Subunit pattern Suitable for diagnostic differentiation. Methods: The 20S proteasomes were isolated from surgical tissue specimens derived from terminal ileum and colon of IBD patients and controls. Spots of 20S proteasomes separated by 2D electrophoresis were analyzed by mass spectrometry. Quick detection of catalytic beta 2, beta 2i, and beta 5i Subunits was performed by incubating proteasomes with biotinylated inhibitor (AdaK(Bio)Ahx3L3VS) and Subsequently by streptavidin-horseradish peroxide. Results: 20S proteasomes were isolated front the human liver, colon. and terminal ileum. Low expression of the immunosubunits beta 1i and beta 2i was found in the liver and colon but high amounts in the small intestine. In colon and liver beta 5i was found to be associated with the constitutive beta 1, beta 2 Subunits. indicating the existence of mixed proteasomes. Further. inflammation in CD but not UC patients induced massive Upregulation of beta 1i and beta 2i in the colon and terminal ileum, indicating the importance of this protein complex as a disease marker. Conclusions: We here show that CD and UC patients display a characteristic pattern of proteasome Subunit composition which can be used as diagnostic tool to differentiate between CD and UC.