The toxicity of carbon nanotubes (CNTs) toward the mitochondria of the kidney is not fully recognized and still needs further research. Apigenin (APG) is known as a flavonoid compound and natural antioxidant. The purpose of this study was to assess the ameliorative role of APG against multiwall CNT (MWCNT)-induced kidney toxicity in rats. The animals were administrated with APG (10 mg/kg) for 2 weeks and then were exposed to MWCNTs (5 mg/m 3 ) in pure and impure forms (10 and 100 nm) for 5 h/day and 5 days/week. Then, mitochondria were isolated from the kidney tissue and mitochondrial toxicity parameters were measured. Decreases in succinate dehydrogenase activity have been reported in all groups exposed to MWCNTs. Results indicated that MWCNTs in both forms and sizes were able to increase the generation of reactive oxygen species, decline mitochondrial membrane potential, induce mitochondrial swelling, and release cytochrome c in isolated kidney mitochondria. The pretreatment of APG decreased all the abovementioned mitochondrial damage and oxidative stress parameters induced by both pure and impure MWCNTs. Our results showed that MWCNTs have the ability to enter the body, subsequently, cross cellular barriers, and reach the kidney as a sensitive organ, which can result in mitochondrial damage in kidney cells including renal tubular cells. In addition, APG can be an effective nutritional antioxidant regimen against MWCNT-induced kidney damage.