Sphincter electromyography (spEMG) is often used as an ancillary test when multiple system atrophy (MSA) is suspected. Our aim was to determine the clinical features associated with spEMG being performed, the influence of the result on the final clinical diagnosis, and its utility as a clinical investigation. A retrospective audit of all cases in the Queen Square Brain Bank between 1989 and 2002 was performed. The clinical features and diagnostic accuracy were compared between patients in whom spEMG was performed and those in whom it was not. From 845 sets of complete clinical records, we identified 37 (4.4%) cases that had been investigated with spEMG. Thirty of these cases had a pathological diagnosis of MSA. Of these 30, 24 had abnormal spEMGs, 5 had a borderline result, and only 1 had a normal spEMG. Sixty-six cases had pathologically proven MSA but no spEMG. Those investigated with spEMG were younger at disease onset (P < 0.001), more frequently male (P = 0.03), and more likely to have had other investigations performed. They had a greater incidence of pyramidal tract signs at final clinical diagnosis, and the final clinical diagnostic accuracy was higher (P = 0.04). Due to the retrospective nature of the study, balanced populations for calculation of sensitivity and specificity were not available. In this selected series of pathologically confirmed cases, investigation with spEMG was one of several factors associated with improved clinical diagnostic accuracy. A normal spEMG is unlikely in pathologically proven MSA, at least in cases with a mean symptom duration of more than 5 years when the test is performed.