Electromyographic studies of the external anal sphincter muscle have received increasing attention in the differential diagnosis of patients with parkinsonism. Based on the fact that the external anal sphincter muscle is partly innervated by fibers that originate in Onuf's nucleus in the segments S2-S4 of the spinal cord, an increased duration of the motor unit potentials (MUPs) and an increased polyphasia may reflect neuronal loss of these lower motor neurons characteristic for multiple system atrophy. We report the results of anal sphincter electromyography in 15 patients with clinically probable multiple system atrophy (MSA) and 10 patients with Parkinson's disease (PD). There was no significant difference between patients with MSA and patients with PD concerning the duration of MUPs, mean number of phases, and rate of polyphasic motor potentials. There was a tendency for a longer mean duration and increased polyphasia in patients with MSA compared to patients with PD. Spontaneous activity was recorded in 11 of 15 patients with MSA occurring especially in patients with MSA of the striatonigral type, but not in patients with PD. In this study, the duration of MUPs and the rate of polyphasia were unreliable criteria in the electrophysiological differential diagnosis of patients with parkinsonism. Abnormal spontaneous activity, although difficult to detect, is a more specific marker for neuronal degeneration of Onuf's nucleus occurring in patients with MSA.