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The present study was performed to evaluate the effect of three natural antioxidants on the adverse effect of methotrexate (MTX) in normal liver cells. TaqMan RT-PCR technology was used to estimate the mRNA expression levels for three genes after rats injection with a single dose of 20 mg/kg b.w MTX or the same MTX dose combined with ginger, silymarin or propolis oral administration. The doses of ginger, silymarin or propolis were similar (200 mg/kg b.w) and were daily administrated to rats for 21 days before MTX injection and four days after MTX injection. The three genes were: cytochrome P450 oxidoreductase (POR) that encodes POR enzyme, caspase 3 (CASP-3) that encodes CASP-3 enzyme and interlukin 6 (IL-6) that encodes IL-6 pro- inflammatory cytokine. Results indicate that the used MTX single dose of 20 mg/kg b.w did not significantly affect POR mRNA expression level in rat liver. Moreover the administration of ginger, silymarin or propolis with MTX did not significantly increase or decrease POR mRNA expression level. Results also reveal insignificant increase in CASP-3 mRNA expression level after MTX injection and also after administration of ginger or propolis with MTX. The administration of silymarin with MTX significantly increased the CASP-3 mRNA expression level. IL-6 mRNA expression level was insignificantly upregulated after injection with MTX and also after administration of silymarin with MTX whereas a significantly upregulation in the IL-6 mRNA expression level was reported after administration of ginger or propolis with MTX. Key words: Methotrexate, ginger, silymarin, propolis, mRNA expression.