This article provides an overview of how transcranial magnetic stimulation (TMS) and positron emission tomography (PET) can be combined. It explains the methodology concerning the combination of TMS with PET and discusses the applications of this combination to study human brain function. TMS represents a nonphysiological means of producing or modulating neuronal activity in the human brain. PET imaging can make an important contribution to the understanding of the mechanisms of action of repetitive TMS and has the potential to determine neural correlates of compensatory plasticity in both healthy subjects and disease states. By using different sources of information, the TMS-PET approach provides insight into the neurophysiological effects of TMS on human brain function. The future use of TMS is to improve the understanding of how the nonphysiological mode of brain stimulation interacts with ‘normal’ activity in the human brain.