In a mouse model the effects of environmental stress on gastrointestinal parameters and the effects of cheese‐whey on the changes induced by stress were studied. Mice were subjected to overcrowding, lack of bedding, overcrowding together with lack of bedding, continuous light, and housing at 30°C. The influence of stress on relative caecal weight, faecal enterobacteriaceae, colonisation resistance (CR), filamentous segmented bacteria in the small intestine, fusiform bacteria in the faeces, and concentration of faecal bile acids was studied. Stress had no influence on relative caecal weight, faecal enterobacteriaceae, and faecal bile acids. Stress did decrease colonisation resistance, presence of segmented filamentous bacteria in the small intestine, and fusiform bacteria in the faeces. Cheese‐whey had no positive effect on the microbiological disturbances caused by stress. The number of filamentous segmented bacteria in the small intestine and fusiforms in the faeces decreased by giving cheese‐whey.