The effects of genetically modified (GM) soyabean meal (SBM) and GM maize on the functional status of the small intestine of broiler chickens was studied. Eight diets were prepared, based on conventional or GM SBM (GTS 40-3-2) combined with non-modified maize cvs. Clarica and PR39 F58 or their isogenic GM (MON 810) counterparts cvs. Bacilla or PR39 F56. Diets were fed in mash form from days 1 to 30 of age to 192 Ross 308 broiler females, assigned to 8 groups and kept in individual cages from day 8 of life. The functional status of the small intestine was studied in 8 birds per group after slaughter. The investigation included morphological evaluation of jejunum and ileum sections, calculation of apoptotic and mitotic indices, and measurement of DNA damage in jejunal epithelial cells. There were no statistically significant differences in morphological parameters of the jejunum and ileum except the width of the tunica mucosa in the jejunum, which was greater in birds fed GM than in those given conventional maize. GM SBM had no effect on the apoptotic and mitotic indices in the crypt area or in villi tips, while GM maize did not affect these indices in the crypt area, but increased the apoptotic index in the villi tips of the jejunum. Neither substituting conventional SBM by GM SBM, nor conventional maize by GM maize induced significant DNA damage in the epithelial cells of the jejunum. Our results indicate that the functional development and maturation of the small intestinal epithelium is not greatly modified by the use of GM SBM and GM maize in broiler diets.