Analysis of changes after ischemia-reperfusion (IR) attack to the small intestine leads to multiple organ dysfunction (multiple organ dysfunction syndrome, MODS) and the subsequent death of patients is a topic for discussion. IR stress affects the endoplasmic reticulum (ER). ER dysfunction induces responses through kinases activation that stimulate anti-apoptotic mechanism, for example Grp78 (Bip) (Yeung et al., 2008) and pro-apoptotic mechanism, for example, activation Gadd153 (Chop) (Allyson et al., 2007). We analyzed the impact of IR damage of epithelium of the small intestine of rats after 1 h ischemia and subsequent 1 h, 24 h and 30 days of reperfusion on the level of apoptotic genes expression (Gadd153) and (Bip). In this study we used RT-PCR for detection of changes in gene expression. Significantly increased levels of mRNA for Gadd153 gene were detected after 1 h ischemia and 1 h reperfusion. The mRNA level of Grp78 gene was increased 24 h after ischemia comparing with the control groups. After 30 days of reperfusion Grp78 was at the level of control groups. Still, it is necessary to analyze the changes in the damaged tissue at the molecular level to define possible pathways leading to the tissue protection.