In the present study, we used fMRI to investigate whether event-related preparatory processes of self-initiated and externally triggered movements differ. Twenty subjects were examined with 1000 T2*-weighted images in two consecutive sessions. During the first session subjects performed self-initiated abductions of the right index finger. For the second session subjects were instructed to perform the movements in response to visual cues. Number and timing of movements were matched between conditions. For statistical inference on multisubject level, random effects analyses were performed. Significantly enhanced activity during self-initiated compared to externally triggered movements was found within the left SMA, the left pre- and sensorimotor cortex, the right putamen, the left anterior cingulate gyrus, and the left inferior parietal lobe. The significantly increased activity during self-initiated in comparison to externally triggered movements might represent differential demands of the two conditions on the neuronal motor net during movement preparation, reflecting utilization of precise knowledge when to move in self-initiated movements. Our results emphasize a possible role of the primary motor cortex for movement preparation as observed in electrophysiological studies, but do not support a specific involvement of the dorsolateral prefrontal cortex as suggested by former block design studies.