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Transcranial magnetic stimulation is becoming increasingly popular to study the rapidly conducting output from the motor cortex. Little is known about the effects of such stimuli on other aspects of cortical function. In the study single magnetic stimuli, subthreshold for movement, produced significant preference for selection of one hand in a forced-choice task. The hand preference depended upon the direction of the induced current. It occurred when the coil was positioned over frontal but not occipital cortex and was not mimicked by weak DC stimulation. Single magnetic stimuli which do not evoke movement can alter high-level motor planning.