Segmental small intestine transplantation (SIT) in rats, using a cuff technique, has achieved a high success rate. However, there have been few reports on the influence of the foreign body reaction to polyethylene cuff on vessel anastomoses and graft after SIT. This study involves the histopathological examination of the site of cuff anastomosis and grafts in the short- and long-term survival of segmental SIT. The data obtained from the suture anastomosis model also served as a control. One week after heterotopic segmental SIT using the cuff technique, orthotopic continuations were carried out in syngeneic combination. Twenty-five of 30 rats surviving >200 days (83.3%) were examined for vessel anastomosis. All arterial anastomoses were patent, but the portovenous anastomoses in 10 grafts (33%) were totally occluded and were associated with the formation of collateral vessels. Histopathological examination demonstrated good patency of the artery and vein anastomotic site in the short term, but granulation, fibrosis, and neovascularization at the anastomosis site surrounding the cuffs in the long-surviving group. However, the grafts appeared to be intact, with normal features of the villi. On the contrary, the site of the sutured anastomosis in the long-survival rats showed no inflammatory reaction. Although a polyethylene cuff caused foreign body reaction, the graft blood supplies were maintained by collateral vessels. Considering the low mortality and high success rate, polyethylene cuff is good for short-term study and an alternative method for long-term SIT experiments.