Hepatotoxicity and nephrotoxicity are common side effects of 5-Fluorouracil (5-FU). The present study aimed to investigate the effects of Silymarin (SLY) on 5-FU induced hepatotoxicity and nephrotoxicity in mice. In our study, 10 mice in each group were randomly divided into four groups as the control group, 5-FU, SLY50+5-FU, and SLY100+5-FU group. SLY50+5-FU and SLY100+5-FU groups were administered at a dose of 50 and 100 mg/kg for seven days, respectively. 5-FU was administered at a dose of 400 mg/kg intraperitoneally on the fourth day. After the applications, the mice were decapitated under anesthesia. The liver and kidney functions which urea, creatinine, AST, ALT, and total bilirubin levels were analyzed in serum. In liver and renal tissues, MDA and GSH levels, SOD, CAT, and GR activity were determined. Also, histopathological and immunohistochemical changes were examined in liver and kidney sections. Urea, creatinine, ALT, AST, and total bilirubin levels increased 5-FU group according to control and prevented to this increases the especially high dose of SLY. 5-FU also causes histopathological and immunohistochemical changes such as degeneration, necrosis, hyperemia, DNA damage, and IL-6 increase in kidney and liver tissue. High doses of SLY prevented these changes caused by 5-FU. As a result of this study, it was determined that SLY has hepatoprotective and nephroprotective effects on 5-FU-induced liver and kidney damage in mice.