The aim of this study was designed to investigate the possible beneficial effects of Nigella sativa (NS) and derived thymoquinone (TQ) on neurodegeneration in hippocampus after chronic toluene exposure in rats. The rats were randomly allotted into one of four experimental groups: A (control), B (toluene treated), C (toluene treated with NS) and D (toluene treated with TQ); each group contain 10 animals. Toluene treatment was performed by inhalation of 3,000 ppm toluene, in a 8 h/day and 6 day/week order for 12 weeks. Control group received 1 ml serum physiologic and the rats in NS and TQ treated groups (C and D) were given NS (in a dose of 400 mg/kg body weight) and TQ (50 mg/kg body weight) once a day orally by using intra gastric intubation for 12 weeks starting just after toluene exposure respectively. Tissue samples were obtained for histopathological investigation. To date, no histopathological changes of neurodegeneration in hippocampus after chronic toluene exposure in rats by NS and TQ treatment have been reported. In this study, chronic toluene exposure caused severe degenerative changes, shrunken cytoplasma, slightly dilated cisternae of endoplasmic reticulum, markedly swollen mitochondria with degenerated cristae and nuclear membrane breakdown with chromatin disorganization in neurons of the hippocampus. The distorted nerve cells were mainly absent in the TQ and NS-treated rats. We conclude that TQ and especially NS therapy causes morphologic improvement on neurodegeneration in hippocampus after chronic toluene exposure in rats. We believe that further preclinical research into the utility of NS and TQ may indicate its usefulness as a potential treatment on neurodegeneration after chronic toluene exposure in rats.