Ileo-rectal anastomosis (IRA), which is frequently used to measure prececal digestibility in pigs, could induce some disturbances of the normal absorptive function. Our aim was to investigate the effects of different IRA surgical procedures on the main histologic characteristics of the small intestine in pigs. The 4 different IRA procedures compared to intact pigs (INT) were the following: either end to end (EE) or end to side (ES) with or without preservation of the ileocecal valve (EEV, EE, ESV, ES respectively). At 147 d after surgery, samples of the wall of the duodenum, jejunum and ileum were taken under anesthesia and histometric examinations were performed on HE- and PAS-colored sections to estimate changes mainly of mucosa and muscle layers. The values recorded for villus length, crypt depth, and whole thickness of the mucosa suggested that the EE procedures disturb the small intestine less than the ES models. A new parameter, called epithelial quotient and calculated as [(villus length/crypt depth)/mitotic index], was proposed to improve the comparisons. According to this quotient, EE procedures did not significantly affect the mucosa of the whole small intestine. An increased density of goblet cells was recorded in all operated pigs along the small intestine, but mainly in the ileum after EE-IRA. The lymphatic follicle area was reduced. These findings, which were in agreement with a reduced mitotic index in the ileum of EE-pigs, indicated a decreased effect of noxious factors on the small intestinal mucosa in IRA-pigs, especially after the EE-IRA procedure. Some atrophic or hypertrophic effects on the muscle layers were related to the absence or preservation of the ileo-cecal valve. Finally it was concluded that i) there was no major disturbance after IRA, and ii) the end to end procedure was most beneficial for the structural integrity of the small intestine.