Background As one of the toxic mechanisms of nanoparticles (NPs), the reactive oxygen species (ROS) generation has been widely studied. Nevertheless, the link between GNPs and antioxidant oxidative stress markers has not been well established. So this study was aimed to evaluate the effect of gold nanoparticles (GNPs) size and exposure duration (3 and 7 days) on antioxidant and oxidative stress markers including reduced glutathione (GSH), super oxide dismutase (SOD), glutathione peroxidase (GPx), glutathione reductase (GR), total antioxidant capacity and malondialdehyde (MDA) in different rat organs. Materials and methods Adult male Wistar-Kyoto rats were randomly divided into 6 groups of 5 animals each. One group served as control and received vehicle only. The 10 nm GNPs (MKN-Au-010 of concentration 0.01%) were used in this study. The GNPs electron density and homogeneity in shape and size was evaluated. Dose of 50 µl of 10 nm NPs in aqueous solution were administered to animals via intraperitoneal administration daily for exposure duration of 3 or 7 days. The rats were sacrificed 24 h after the last injection of GNPs. The specimens of liver, lung, kidney and heart were collected for biochemical analyses. Results The GPx, total antioxidant capacity, GSH and MDA levels significantly increased after intraperitoneal administration of 10 nm GNPs for exposure duration of 3 and 7 days in the organs of rats compared with the control. The GR and SOD levels significantly decreased after intraperitoneal administration of 10 nm GNPs for exposure duration of 3 and 7 days in the organs of rats compared with the control. Conclusions The NPs have the potential to interact with the biological system and cause undesirable effects. One of these damaging effects could be the disturbance in the natural balance between oxidative stress and antioxidant defense indices which in turn can lead to various pathological effects. The oxidative stress has been identified as a likely mechanism of NPs toxicity. This study demonstrates that the increased production of ROS after intraperitoneal administration of GNPs into rats might attributed to increased production of GPx, total antioxidant capacity, GSH and MDA levels, and to decrease production of GR and SOD levels.