The inclusion of soybean meal (SBM), especially in the diet of Atlantic salmon, induces an inflammatory response of the distal intestinal mucosa, known as SBM-induced enteritis. A semi-quantitative scoring system was developed to assess the extent of the morphological changes observed in this study. The influence of SBM feeding has been investigated taking into account several dietary and non-dietary factors possibly involved in the induction of the disorder. It has been found that the severity of enteritis and its kinetics are dose-dependent. Electron microscopy studies indicated a block of the endocytosis process and a strong decrease of the microvilli length. Comparative studies were carried out in an omnivorous species and for the first time ever reported, the results suggested that the symptoms of enteritis also occur in common carp. Contrary to the observations in studies with Atlantic salmon, the common carp started to recover from week four onwards. Several cytokines were presumed to influence this process and they were correlated to the modulation of the inflammatory process triggered by the SBM-containing diet. The influence of different factors was measured according to the degree of enteritis developed. Low temperature (8 °C vs. 12 °C) seems to delay the onset of the symptoms. On the other hand, it was suggested that SBM-induced enteritis was not strongly influenced by either salinity or age. The extent of enteritis in Atlantic salmon depends on the origin and/or the processing of the soybeans. The morphological changes observed were induced when soyasaponins were fed to Atlantic salmon alone or in combination with other soybean components suggesting their possible role on the induction of enteritis. The actual causative components and its mechanisms of action need further research. It is concluded that the etiology and further development of SBM-induced enteritis is related to dietary factors rather than non-dietary factors. SBM inclusion levels and the commercial source used for the diet formulation have a great impact on the severity of the disorder, mainly affecting the endocytosis process. This thesis evidenced that the endocytosis block is directly related to the disappearance of the supranuclear vacuoles, which can be considered as the most striking feature in the onset of enteritis.