BackgroundTranscranial magnetic stimulation (TMS) is a valuable technique for assessing the function of the motor cortex and cortico-muscular pathways. TMS activates the motoneurons in the cortex, which after transmission along cortico-muscular pathways can be measured as motor-evoked potentials (MEPs). The position and orientation of the TMS coil and the intensity used to deliver a TMS pulse are considered central TMS setup parameters influencing the presence/absence of MEPs. New MethodWe sought to predict the presence of MEPs from TMS setup parameters using machine learning. We trained different machine learners using either within-subject or between-subject designs. ResultsWe obtained prediction accuracies of on average 77% and 65% with maxima up to up to 90% and 72% within and between subjects, respectively. Across the board, a bagging ensemble appeared to be the most suitable approach to predict the presence of MEPs. ConclusionsAlthough within a subject the prediction of MEPs via TMS setup parameter-based machine learning might be feasible, the limited accuracy between subjects suggests that the transfer of this approach to experimental or clinical research comes with significant challenges.