Background: In this study, the protective effect of thymoquinone (TQ) and Nigella sativa seeds oil (NSO) was evaluated against oxidative damages induced by ethanol in rats. Methods: Animals were treated with ethanol 40% daily by gavages once a day for 4 weeks. NSO and TQ were injected intraperitoneal once a day for 4 weeks. The histopathological examination of liver, kidney, brain and heart was done at the end of 4 weeks. Biochemistry tests such as level of serum liver enzymes (ALT, AST, ALP), triglyceride, cholesterol, LDL, HDL were measured. Malondialdehyde (MDA) level and glutathione (GSH) content in the liver and kidney were also evaluated. The level of specific biomarkers such as TNF-α and IL-6 in liver were measured. Apoptosis was assessed by evaluating the amounts of Bax, Bcl-2, caspase 3, caspase 8 and caspase 9 proteins in liver and kidney tissues by western blotting. Quantitative real-time RT-PCR was used to evaluate the expression of Bcl-2 and Bax. Results: Ethanol induced hepatotoxicity and nephrotoxicity as evidenced by histophatological damages, and it also increased the level of ALT, AST and ALP. Data showed that MDA level was significantly increased while GSH content was significantly decreased in the liver and kidney of ethanol-treated rats. The levels of TNF-and IL-6 as specific biomarkers were significantly increased. These effects were associated with increased apoptosis by induction of the expression of Bax/Bcl2 ratio (both protein and mRNA level) and activation of caspase 3, caspase 8 and caspase 9 in liver and kidney. However, the increase in caspase 9 and mRNA level of Bax/Bcl2 ratio in kidney were not statistically significant. The concurrent administration of NSO or TQ and ethanol (3 g/kg) improved the toxic effects of ethanol on kidney and liver. Conclusion: NSO and TQ may prevent ethanol-induced oxidative stress and have protective effects against ethanol-induced toxicity in rat through attenuating lipid peroxidation, increasing GSH content and inhibiting increase of a specific biomarker (IL-6) level. The black cumin and its constituents may reduce apoptosis by modulating Bax/Bcl-2 ratio, and the level of caspase 3, caspase 8 and caspase 9.