Brain imaging studies demonstrate increasing activity in limb motor areas during early motor skill learning, consistent with functional reorganization occurring at the motor output level. Nevertheless, behavioral studies reveal that visually guided skills can also be learned with respect to target location or possibly eye movements. The current experiments examined motor learning under compatible and incompatible perceptual/motor conditions to identify brain areas involved in different perceptual-motor transformations. Subjects tracked a continuously moving target with a joystick-controlled cursor. The target moved in a repeating sequence embedded within random movements to block sequence awareness. Psychophysical studies of behavioral transfer from incompatible (joystick and cursor moving in opposite directions) to compatible tracking established that incompatible learning was occurring with respect to target location. Positron emission tomography (PET) functional imaging of compatible learning identified increasing activity throughout the precentral gyrus, maximal in the arm area. Incompatible learning also led to increasing activity in the precentral gyrus, maximal in the putative frontal eye fields. When the incompatible task was switched to a compatible response and the previously learned sequence was reintroduced, there was an increase in arm motor cortex. The results show that learning-related increases of brain activity are dynamic, with recruitment of multiple motor output areas, contingent on task demands. Visually guided motor sequences can be linked to either oculomotor or arm motor areas. Rather than identifying changes of motor output maps, the data from imaging experiments may better reflect modulation of inputs to multiple motor areas.