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Background Surgery of thoracoabdominal aortic aneurysms (TAAA) is associated with high incidence of serious complications. Ischemia/reperfusion (I/R) injury may be responsible for these complications. We investigated the effect of degree of anticoagulation on remote organ I/R injuries and whether heparin is protective against I/R injury in addition to its anticoagulant properties. Methods Spraque Dawley rats were used to determine both liver and kidney concentrations of HSP- 70,IL-6, MPO in four groups: ischemic control (operation with cross-clamping and intraperitoneal administration of 0.9% saline, n = 7), sham (operation without crossclamping, n = 7), heparin (ACT level about 200), and high dose heparin (ACT level up to 600). Histological analyses of the organs were performed. Results Histopathological evaluation of kidney presented significant differences between groups with regards to the cytoplasmic vacuole formation, hemorrhage, tubular cell degeneration and tubular dilatation while heparinized group had best results. The kidney MPO and HSP-70 levels significantly decreased (p < 0.05), but IL-6 level was not significant (p > 0.05) in heparinized group when compared to ischemic control group. No statistically significant intergroup differences were detected in the tissue samples of liver. Immunohistochemical markers of the liver were compared and no statistically significant difference was found among the groups. Conclusion Heparin is an important anticoagulation agent in TAAA surgical procedures but the use of higher levels of heparin in the present study revealed no beneficial effects. Bleeding complications is much less when heparin is used in the real-world clinical practice as ACT levels of 200. [ABSTRACT FROM AUTHOR]