In broiler chickens, a diet where the major cereal types are wheat, rye and/or barley has a lower digestibility compared with a diet in which maize is the major cereal type. In the present study, the effects of two different dietary cereal types, maize v. wheat/rye, on host factors (inflammation and gut integrity) and gut microbiota composition were studied. In addition, the effects of low-dose Zn-bacitracin supplementation were examined. Broilers given a wheat/rye-based diet showed more villus fusion, a thinner tunica muscularis, more T-lymphocyte infiltration, higher amount of immune cell aggregates in the mucosa, more and larger goblet cells and more apoptosis of epithelial cells in the mucosa than those given a maize-based diet. Adding Zn-bacitracin generally reversed these alterations. The microbiota composition was analysed by the use of terminal-restriction fragment length polymorphism, showing changes in the microbiota composition depending on the cereal type used in the diets. The effect of the change of cereal type on the gut microbiota composition was larger than that of Zn-bacitracin supplementation. In conclusion, a wheat/rye-based diet evoked mucosal damage, an alteration in the composition of the microbiota and an inflammatory bowel type of condition.