The intracellular accumulation of gentamicin acts on mitochondria directly (by increasing oxidative stress) and indirectly (by increasing the proapoptotic BAX gene expression levels) and thus activates intrinsic pathway of apoptosis. This study intended to investigate the probable prophylactic effect of wheat germ as a nephro-protective agent in relation to vitamin E as a well-known natural antioxidant on a nephrotoxic model induced by gentamicin. Forty male Sprague Dawley rats were divided randomly into four groups; of 10 rats each: control group, gentamicin group (120 mg/kg/day i.p. for 15 days), vitamin E group (200 mg/kg orally for 45 days) and wheat germ group (20% of the diet for 45 days). Gentamicin injection was started on the 30th day for both groups (3) and (4). It was noticed that wheat germ significantly decreased BAX/BCL-2 ratio. The significant decrement in MDA level and the significant increment in total antioxidant capacity (TAC) level and catalase (CAT) activity of wheat germ treated rats reflecting its antioxidant activity. Additionally, the wheat germ succeeded in improvement of the kidney function of rats of this group which was manifested by amelioration of deteriorated serum creatinine, urea, sodium and potassium levels. In conclusion, the efficacy of wheat germ as anti-apoptotic and antioxidant was higher than that of vitamin E and it effectively protected against the direct and indirect toxic effects of gentamicin on kidney through regulation of BAX-BCL-2 gene expressions and further inhibition of mitochondrial cytochrome c translocation into cytosol.