Introduction: Widespread agricultural use as well as increasing number of suicidal or accidental ingestion of paraquat in the last few years enhance the necessity to evaluate the mechanism of action and the complications, especially neuronal side-effects, of this herbicide. The aim of this study was to evaluate the histopathological alterations of the substantia nigra after paraquat intoxication in rats. Materials and Methods: 28 adult Wistar rats were randomly divided into three experimental and one control groups. Paraquat at different doses (10, 15 and 20 mg/kg) were injected intraperitoneally once a week for three consecutive weeks to experimental groups; normal saline was injected to control group. After 28 days, the brains were removed and sections from the compact part of the substantia nigra were stained by toluidine blue. Results: A significant enhancement of the number of dark neurons in the substantia nigra was observed in rats receiving 15 and 25 mg/kg of paraquat compared to control group. Conclusion: Our findings point to the harmful effects of paraquat on neurons of the substantia nigra. This suggests paraquat toxicity as a risk factor for neurological disorders, such as Parkinson’s disease.