The current study investigated the effects of the inclusion of modern hybrid rye (Brasetto variety) to a corn–wheat-based diet, with or without xylanase, on the absorptive surface of the small intestine of broilers. A total of 224 one-day-old male Ross 308 broiler chicks were randomly divided into four experimental groups with seven replicate cages of eight birds/replicate. A 2 × 2 factorial study design was used, with rye inclusion (0% or 20%) and xylanase supplementation (0 or 200 mg/kg of feed) as factors. Inclusion of rye increased duodenal and ileal crypt depth, villi height, the villus-to-crypt ratio and absorption surface area (p < 0.05), and ileal mucosa thickness and crypt width (p < 0.05). Xylanase supplementation attenuated the effects of rye in the duodenum and ileum and decreased the villi height and villus-to-crypt ratio in the jejunum (p < 0.05). Rye and xylanase had no effect on the spatial distribution of claudin 3 and ZO-1 protein, but xylanase supplementation reduced the amount of claudin 3 in the duodenum and jejunum (p < 0.05). The findings of this study indicate that 20% inclusion of modern hybrid rye to the diets of broilers improved the structure of the duodenum and ileum, but these effects were attenuated by xylanase supplementation.