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OBJECTIVE The aim of this study was to investigate the effect of daidzein against intestinal ischemia-reperfusion injury in rats. MATERIALS AND METHODS Thirty male Wistar albino rats with a mean weight of 200-250 gr were used. Animals were categorized into sham, ischemia-reperfusion (IR), and IR+Daidzein group. 3-hour ischemia of intestine was created by occluding superior mesenteric artery and then left for 3-hour reperfusion. In IR+daidzein group, after ischemia, 50 mg/kg daidzein was orally administered to the animals. Blood samples were collected for biochemical assays. Intestine tissues were excised for histopathologic and immunohistochemical processing. RESULTS Malondialdehyde (MDA) increased, and Catalase (CAT) and Glutathione (GSH) decreased after IR in intestine tissue. Daidzein treatment decreased MDA and increased CAT and GSH level in IR+Daidzein group. Histopathologically, sham group showed normal intestinal tissue histology. In IR group, epithelial and villi degeneration, edema, leukocyte infiltration, vascular dilatation and congestion was observed. After Daidzein treatment, these pathologies were improved. The caspase-6 expression was mainly negative in sham group. After IR, caspase-6 reaction was very high in IR group. Daidzein reduced caspase-6 expression in IR+Daidzein group. Ki67 immune staining was negative in the sham group. In IR group, Ki67 expression was increased in inflammatory cells, deep glandular cells and in some goblet cell nuclei. In IR+Daidzein group, Ki67 expression was decreased due to reduced inflammation. CONCLUSIONS IR injury causes oxidative stress, apoptosis and inflammation. Daidzein treatment improved histopathology against intestinal IR.