Ischemic-reperfusion (IR) injury of the small intestine makes a serious complications associated with various surgical procedures and is related to changes in motility, secretory activity and structural alterations. Preconditioning can reduce range of this damage. The aim of the experimental study was to determine the influence of ischemic preconditioning (IPC) on IR injury on jejunal epithelial layer. Wistar rats (n = 56) were divided in two experimental groups. IR group was subjected to 60 min ischemia of cranial mesenteric artery and followed by reperfusion periods: 1,4,8,24 h (IR1, IR4, IR8, IR24). Group with ischemic preconditioning (IPC+IR) was subjected to two subsequent ischemic attacks (12 min) with 10 min of reperfusion between them, and after 2nd attack ischemia was induced for 60 min followed by relevant reperfusion period. IPC showed the protective impact on the jejunal tissue architecture after 1 h reperfusion, when in IR1 group the highest and significant damage was observed (p < 0.001) in contrast to IPC+IR1 group. Histopathological damage of the intestine in pretreated groups was postponed to 4 h of reperfusion. Protective effect of IPC together with later accumulation of injury signs were confirmed by weaker impact on goblet cell (p < 0.001) and Paneth cell populations (p < 0.05).The increased cells proliferation in preconditioned groups came later, but stronger after 8 h of reperfusion (p < 0.001) and after 24 h of reperfusion still remained at the high activity level (p < 0.001). Our experimental results on the histopathological changes in the jejunum during ischemic preconditioning proved that IPC may have a positive effect on maintaining intestinal barrier function.