Transcranial magnetic stimulation (TMS) combined with electroencephalography (EEG) is a powerful technique for non-invasively studying cortical excitability and connectivity. The combination of TMS and EEG has widely been used to perform basic research and recently has gained importance in different clinical applications. In this paper, we will describe the physical and biological principles of TMS-EEG and different applications in basic research and clinical applications. We will present methods based on independent component analysis (ICA) for studying the TMS-evoked EEG responses. These methods have the capability to remove and suppress large artifacts, making it feasible, for instance, to study language areas with TMS-EEG. We will discuss the different applications and limitations of TMS and TMS-EEG in clinical applications. Potential applications of TMS are presented, for instance in neurosurgical planning, depression and other neurological disorders. Advantages and disadvantages of TMS-EEG and its variants such as repetitive TMS (rTMS) are discussed in comparison to other brain stimulation and neuroimaging techniques. Finally, challenges that researchers face when using this technique will be summarized.
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