Radiation induced colitis is one the most common clinical issue for patients receiving radiotherapy. For this reason, we aimed to investigate the effect of antioxidant-effective flavonoids hesperidin and quercetin on the intestinal damage induced by radiation in this study. TNF-alpha, interleukin-10 (IL-10), heat shock protein 70 (HSP 70) and caspase 3, 8, 9 markers of apoptotic pathways were measured in the colon tissues of irradiated acute intestinal damage by enzyme-linked immunosorbent assay (ELISA). Irradiation of rats caused a significance increase of TNF-alpha, caspase 3/8/9 and decrease of IL-10 concentrations. Hesperidin and quercetin treatment resulted in decreased levels of TNF-alpha and increased levels of IL-10. Quercetin significantly decreased caspase 3/8/9 levels. Hesperidin produced a decreased of caspase 3/8/9 levels compared with irradiation group but this was statistically not significant. Only significant alteration of HSP 70 were seen in hesperidin treated rats. Further studies are needed to elucidate the mechanism by which flavonoids induced signaling provides protection against apoptosis and inflammation.