This study evaluates the effect of temperature on the development of intestinal disorders when Atlantic salmon are fed soybean meal (SBM). In this study 20% of the dietary fishmeal was replaced by solvent-extracted Hipro SBM. Atlantic salmon reared at two different water temperatures (8 °C and 12 °C), were fed a control diet and an experimental diet for 20 days. Samples were taken at days 7 and 20. The extent of the morphological changes was assessed using a semi-quantitative scoring system developed for this purpose. The study demonstrates that enteritis is affected by temperature. The intestinal disorders were more severe in fish reared at 12 °C compared with those reared at 8 °C. It can be concluded from this study that temperature changes the speed but not the type of SBM-induced enteritis expressed as a delay on the response when Atlantic salmon are kept at lower temperatures.