PURPOSE: Our aim was to determine whether the mucosa of a canine jejunal pouch used as a rectal substitute after proctocolectomy retains its morphologic features better than the mucosa of a canine ileal pouch so used. METHODS: Among ten dogs that underwent proctocolectomy, five had a jejunal pouch-distal rectal anastomosis and five an ileal pouch-distal rectal anastomosis. After six months, the animals were killed, the intestinal pouches and portions of unaltered distal ileum were removed, and a blinded, mucosal morphometric analysis was performed. RESULTS: The mucosa of the jejunal pouches had an overall thickness (mean ± standard deviation, anterior and posterior walls, 1,300 ± 140 μm), villous height (286 ± 46 μm), and crypt depth (790 ± 77 μm) greater than that of the ileal pouches (920 ± 170, 208 ± 47, and 530 ± 130 μm, respectively; P < 0.05). Moreover, the mucosal thickness of the jejunal pouches was similar to that of the distal ileum proximal to the pouch (1,200 ± 200 μm; P > 0.05), whereas the mucosal thickness of the ileal pouch was thinner (P < 0.05). CONCLUSIONS: The jejunal mucosa retains its major morphometric features when the jejunum is used as a rectal substitute after proctocolectomy. In contrast, the ileal mucosa atrophies when the ileum is so used.