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