The TMS-evoked potentials are derived from the coregistration of transcranial magnatic stimulation and electroencephalography (TMS-EEG) and are now an established method to study effective connectivity both in healthy and pathological brain. The activation induced by the TMS in the targeted area propagates to anatomically and functionally connected regions and the propagation can be traced with millisecond temporal resolution by means of EEG. Importantly, the information about the temporal pattern of the responses induced by the TMS contributes to defining the causal relationships in the connections across brain areas. Here, we will present current TMS-EEG studies and we will describe what is known about the origin of TEPs, their relation with structural and functional measures of long-range connections. Moreover, we will highlight the types of information that can be obtained from TEPs for studying effective connectivity. Finally, we will present ongoing challenge and current debates on the TEPs approach.