Previous studies based on single sections have suggested a significant correlation between pigmented neuronal loss in the substantia nigra (SN) and clinical features in Parkinson's disease (PD). However, disector (DS) counts-unbiased and accurate stereological estimates have not been available. To evaluate total neuron numbers in the pars compacta of the substantia nigra (SNpc) in relation to clinical features, we estimated the neuron counts in the SNpc by the DS method in brain samples from 12 controls and 12 PD patients. The total number of pigmented neurons in the whole SNpc was significantly reduced in PD patients (to 45% of the control mean, P < 0.001). The density of pigmented neurons (neuron/mm3) was reduced to 51% of the average control value (P < 0.001). No significant difference was seen in the volume (mm3) of the SNpc between PD patients and controls. Furthermore, the total number of pigmented neurons in the SNpc showed a significant negative correlation with the duration of disease (r = -0.86, P < 0.001) and with the stage of disease (r = -0.58, P < 0.05) in PD patients. Using an unbiased neuron counting method, these relationships, for the first time, demonstrate that the more severe pigmented neuronal loss in the SNpc is associated with the longer duration and the more severe stage of disease in PD patients.