The alimentary tract is a possible site where pathogens and toxins can enter. The alimentary tract is protected, amongst others, by mucus. In this study, tissue samples and crude mucus preparations from different parts of the intestinal tract of Cyprinus carpio (from intestinal bulb onto the hindgut) were examined using histological, histochemical and biochemical techniques. Furthermore, the response of the intestinal mucosal layer and intestinal mucus of C. carpio to acute soybean meal (SBM)-induced enteritis was investigated. In the present study, an indication for a different protein core of mucus high molecular weight glycoproteins (HMGs) for first and second segment could not be found. However, differences in mucus glycosylation could be found. Along the gut axis, the size of the major protein peaks were not similar, which can be caused by a different glycosylation. Also, differences in staining for the antimicrobial peptide beta-defensin 2 were found. Furthermore, changes in HMGs upon SBM diet were found similar to those found in inflammatory bowel disease (IBD) in humans. Initial changes include: changes in mucin composition, the presence of BD3 and of bacteria in internal organs. After the initial changes, all values measured returned back to the initial pre-SBM diet values.