Rotenone caused endolysosomal deficits in rats. The number of late endosomes and lysosomes in nigral dopaminergic neurons were assessed by immunohistochemistry using Lamp1 and M6PR for late endosomes and lysosomes and TH for dopaminergic neurons. The number of late endosomes (Lamp 1+, M6PR+) and lysosomes (Lamp 1+, M6PR−) in nigral dopaminergic neurons of rats dosed with vehicle, acute or endpoint rotenone (A). Quantification for the average number of late endosomal and lysosomal puncta in nigral dopaminergic neurons in rats dosed with acute and endpoint rotenone; n = 4/grp (B–C). Lysosomal and non-lysosomal cathepsin D immunoreactivity was assessed in nigral dopaminergic neurons using specific markers. The number of lysosomal cathepsin D (Lamp 1+, cathepsin D+) and non-lysosomal cathepsin D (Lamp 1−, cathepsin D+) in nigral dopaminergic neurons of rats dosed with vehicle, acute or endpoint rotenone (D). Quantification for average number of cathepsin D puncta per nigral dopaminergic neuron; n = 4/grp (E). Quantification for the average number of lysosomal cathepsin D puncta per dopaminergic neuron assessed using Pearson correlation coefficient (F). Data are analyzed using unpaired t-test ** p < .01, *** p < .001, **** p < .001 graphs are expressed as mean ± SEM. Symbols represent individual brains.