Objective To investigate the effects of quercetin (Q) and rutin on 5-fluorouracil (5-FU)-induced hepatotoxicity. Methods The control group was corn oil. The 5-FU group rats were corn oil and injected intraperitoneal 5-FU 50 mg/kg. Groups rutin 50 + 5-FU and rutin 100 + 5-FU were respectively 50 mg/kg and 100 mg/kg rutin. These groups were given 5-FU (50 mg/kg) in the 18th day. The group rutin 100 was rutin (100 mg/kg i.g.). Groups Q50 + 5-FU and Q100 + 5-FU were respectively 50 mg/kg and 100 mg/kg quercetin. These groups were given 5-FU (50 mg/kg) in the 18th day of quercetin application. The group Q100 was quercetin (100 mg/kg i.g.). In the end of experimental applications, blood was collected from anesthetized rats. Results The MDA level was significantly higher in the 5-FU group compared with control group, and determined to be decreased in other groups. GPx and GSH levels were significantly decreased in the 5-FU group compared to the control, rutin 100 + 5-FU and Q100 + 5-FU groups. AST, ALT, LDH and ALP levels in the serum were significantly increased in the 5-FU group compared with the other groups. The results from this analysis show that while the caspase-3 level increases in the 5-FU group, it decreases in the Q50 + 5-FU, Q100 + 5-FU, rutin 50 + 5-FU and rutin 100 + 5-FU groups. Bcl-2 level decreased in the 5-FU group compared to the control group, but increased in the rutin 100 + 5-FU, Q50 + 5-FU and Q100 + 5-FU groups. Conclusions In this study it was determined that the rutin and Q have protective effects on 5-FU-induced hepatotoxicity.