Abstract. Objectives: The aim of the study was to explore the protective effect of the flavonoids rutin, silymarin, and puerarin against aluminum (Al)-induced liver and kidney toxicity. Materials and methods: 80 male rats of SPF grade were randomly divided into 8 groups: control, Al-treated, low-dose rutin, high-dose rutin, low-dose silymarin, high-dose silymarin, low-dose puerarin, and high-dose puerarin. The control group received 1 mL/kg/day saline solution for 12 weeks. The other groups were exposed to Al at a dose of 281.40 mg/kg/day orally for 4 weeks. Then, they respectively received 1 mL/kg/day saline solution, 100 mg/(kg×day) rutin, 200 mg/(kg×day) rutin, 100 mg/(kg×day) silymarin, 200 mg/(kg×day) silymarin, 100 mg/(kg×day) puerarin, and 200 mg/(kg×day) puerarin for 8 weeks. The tested chemicals were given by gavage. At the end of the exposure period, iron (Fe), copper (Cu), zinc (Zn), calcium (Ca), and magnesium (Mg) were determined by atomic absorption spectrophotometry. Results: Compared with the control group, the Al-treated rats’ Fe, Mg, Ca, and Zn concentrations in the liver were lower, and Fe, Mg, and Ca levels were lower in the kidney (p < 0.05). Treatment with rutin, silymarin, or puerarin can improve the content of Fe, Mg, and Ca in liver and kidney of rats exposed to Al (p < 0.05). High-dose flavonoids were more effective than low-dose flavonoids. Conclusion: The flavonoids rutin, silymarin, and puerarin have a protective effect on essential elements in rat liver and kidney exposed to Al.