Activity of the prefrontal cortex (PFC) has been observed in previous block-design brain imaging studies of self-initiated movements. However, the meaning of these activations remained unclear. A functional MRI experiment was carried out, which utilized an epoch and an event-related analysis approach to the data. We hypothesized that event-related activity of the PFC would argue for a contribution to movement preparation. In contrast, epoch-, but not event-related activity pointed to tonic activations, probably reflecting enhanced attentional states or working memory processing. Twenty-one subjects were examined with 845 T2*-weighted images. During active phases, subjects were instructed to perform self-initiated movements of the right index finger with intertrial intervals of about 8 s. On single subject level, epoch- and event-related regressors were entered into a combined model, estimating the exclusive contribution of either regressor. For statistical inference on multisubject level, random effects analyses were performed. For the epoch regressor, activity within the right dorso- and ventrolateral prefrontal cortex, the bilateral insula, and the right inferior parietal lobe was observed. The event-related regressor detected activity within the right inferior parietal lobe, ventral from the activity found with the epoch regressor. The present results indicate a condition-, but not a movement-related function of the PFC in self-initiated movements. Furthermore, anatomically distinct regions within the inferior parietal cortex seem to be involved in condition-specific and movement-related processes. The observed condition-specific activations are suggested to reflect attentional or working memory processes, supervising task performance, rather than movement preparation or initiation.