【Abstract】 Objective To investigate the protective effect of thymoquinone on intestinal ischemia reperfusion injury in rats. Methods Fortyfive male SD rats were randomly divided into Shamoperation control group (group A), ischemia reperfusion group (group B) and ischemia reperfusion+thymoquinone group (group C). Intestinal ischemia reperfusion model was established in group B and C. Thymoquinone (50 mg /kg ) was injected intraperitoneally followed reperfusion in group C. The pathological changes of the intestine were observed by HE staining. MDA and SOD content were determined. Cell apoptosis index was detected by dUTP nick end labeling. The expression of caspase3, Bax and Bcl2 in intestinal tissue were detected by RTPCR. Results Group B showed intestinal villus disorderly arrangement, intestinal mucosa epithelia necrosis thymoquinone treatment significantly improved the above changes. AI in group A，group B and group C were (453±028)％, (2173±117)％ and (953±096)％, respectively. The SOD activities were (13537±334), (7645±139) and (9513±164)U/mg, respectively. MDA were (283±036), (923±078) and (497±045)nmol/mg. Compared with group A, the mRNA expression of Bax and caspase3 were significantly increased, and the mRNA expression of Bcl2 was decreased in group B (P＜005). Compared with group B, the expression of Bcl2 in was obvious increased, and the expression of Bax and caspase3 decreased in group C(P＜005). Conclusion Thymoquinone reduces the level of oxidative stress and inhibits the apoptosis. Thus, it plays a protective role in the process of intestinal ischemiareperfusion injury.