Excitability and effective connectivity are key parameters of cortical circuits' functioning. Moreover, alterations of these parameters have been suggested to underlie neurologic and psychiatric conditions. Transcranial Magnetic Stimulation (TMS) combined with neuronavigation systems, electroencephalography (EEG), and reliable reconstruction of cortical generators allows to directly measure cortical excitability and effective connectivity, noninvasively and with the appropriate temporal resolution (milliseconds). Here, the main technical challenges that have to be dealt with to efficiently combine navigated TMS with EEG on human subjects and a step-by-step experimental procedure to perform a successful TMS/EEG measurement are presented. Finally, ad hoc analytical tools to extract indices of excitability and effective connectivity from TMS/EEG data are described together with examples of their application.