In the last decade transcranial magnetic stimulation (TMS) has been the subject of more than 20,000 original research articles. Despite this popularity, TMS responses are known to be highly variable and this variability can impact on interpretation of research findings. There are no guidelines regarding the factors that should be reported and/or controlled in TMS studies. This study aimed to develop a checklist to be recommended to evaluate the methodology and reporting of studies that use single or paired pulse TMS to study the motor system. A two round international web-based Delphi study was conducted. Panellists rated the importance of a number of subject, methodological and analytical factors to be reported and/or controlled in studies that use single or paired pulse TMS to study the motor system. Twenty-seven items for single pulse studies and 30 items for paired pulse studies were included in the final checklist. Eight items related to subjects (e.g. age, gender), 21 to methodology (e.g. coil type, stimulus intensity) and two to analysis (e.g. size of the unconditioned motor evoked potential). The checklist is recommended for inclusion when submitting manuscripts for publication to ensure transparency of reporting and could also be used to critically appraise previously published work. It is envisaged that factors could be added and deleted from the checklist on the basis of future research. Use of the TMS methodological checklist should improve the quality of data collection and reporting in TMS studies of the motor system.