We aimed to investigate the effects of thymoquinone (TQ) against Doxorubicin (DOX)-induced toxicity in liver, lung, kidney, testes, diaphragm and stomach tissues of rats. Healthy twenty-eight Wistar albino male rats aged three months, were divided into four groups, each containing seven animals: Group 1: Control (C group); the rats were injected intraperitoneally with saline 5 times every other day and given by gavage to the vehicle solution Group 2 (T group): Rats treated with thymoquinone (10mg/kg given by gavage), Group 3 (D group): Rats treated with doxorubicin were injected intraperitoneally (3mg/kg) and Group 4 (DT group): Rats treated with doxorubicin (injected intraperitoneally with 3mg/kg DOX) and thymoquinone (10mg/kg given by gavage). Group 2 (T group): TQ (10mg/kg) was administered by gavage at 24-hour intervals for 4 weeks. Saline (i.p.) was injected to rats 5 times every other day. Group 3 (D group): The rats were injected with 3 mg/kg DOX (i.p.) 5 times every other day. In addition, vehicle solution was administered by gavage at 24-h intervals for 4 weeks. Group 4 (DT group): Rats were injected with 3mg/kg DOX (i.p.) 5 times every other day. TQ (10mg/kg) was administered by gavage at 24-h intervals for 4 weeks. At the end of the experiment, the animals were euthanized with sodium pentobarbital (50 mg/kg) and their lung, liver, stomach, kidney, diaphragm and testicular tissues were removed for the measurement of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA) levels. It was observed that DOX administration (in group D) increased lipid peroxidation and decreased antioxidant enzyme levels in the peripheral tissues of rats. It was determined that TQ treatment (in the DT group) given with DOX decreased lipid peroxidation and increased antioxidant enzyme levels. In our study, it was determined that TQ treatment eliminated the toxic effects of DOX and the protective effects of TQ were revealed.