Three-dimensional structural parameters correlate better with the intestinal function compared to two-dimensional structural parameters. The objective of the present study was to investigate the three-dimensional morphometrical features of the small intestine in rabbits using a design-based stereology. Five adult male New Zealand rabbits were used in this research. The total volume, volume fraction of different layers, internal surface area, villus and circular folds amplification factors were estimated in the whole and various segments of the small intestine. The small intestine volume was estimated to be 59.57 ± 8.57 cm3. The jejunum and ileum showed the most and the least total volumes, respectively (p < 0.05). The volume fractions of the tunica mucosa, tela submucosa and tunica muscularis were 62.57% ± 2.78%, 21.11% ± 2.01% and 16.25% ± 0.94%, respectively. The minimum volume of the tela submucosa was observed in the ileum (p < 0.05) and the fractional volume of the tunica muscularis in the ileum was significantly more than those of other segments (p < 0.05). The surface area of the entire small intestine was estimated to be 8302.31 ± 1872.39 cm2. The jejunum and ileum segments showed the most and the least surface areas, respectively. The increase in the intestinal surface area attributable to the presence of villi was estimated to be 6.82 ± 0.84, and that for circular folds was accounted for 1.36 ± 0.09. The largest amplification factors of villi and circular folds were observed in the duodenum and ileum, respectively. Our data presented the three-dimensional morphometry of the small intestine of the rabbit as a translational model and provided basic findings for the diagnosis and treatment of intestinal diseases in this species.