<p>The amplitude of the motor-evoked potentials (MEPs) induced by transcranial magnetic stimulation (TMS) is primarily influenced by the orientation of the stimulation coil, while its influence on other MEP features is not well known. Accordingly, this study investigated how the TMS coil orientation affects a comprehensive set of MEP features, including its size, timing, duration, and polyphasia. Nine healthy volunteers were recruited. Three single-pulse TMS sessions were applied to the left hemisphere’s first dorsal interosseous muscle hotspot. The coil was rotated from − 135º to 135º at this location relative to the predefined optimal stimulation angle. The first two sessions were conducted at the same hotspot, and the third at the remapped hotspot. Four levels of analysis were performed: intra-session, inter-session, inter-subject, and features grouped from all MEPs. The timing-related features of MEP were least affected by coil orientation and were intrinsic to each subject, whereas its size-related features varied significantly across subjects. The first two principal components of the MEP waveform accounted for 91.3% ± 3.0% of each dataset’s total variation, indicating intra-session consistency of MEP waveforms. MEP waveforms were comparable intra- and inter-session and slightly different across subjects. Our study provides a comprehensive analysis of how coil orientation affects MEP features waveform morphology and complements previous studies that evaluated only the effects on MEP peak-to-peak amplitude and onset latency. Size-related MEP features varied with coil orientation, which likely changes the effective stimulation intensity at the cortical target, while timing-related features and the dominant waveform morphology were less affected. Furthermore, MEP waveforms were highly consistent across sessions within subjects and differed only slightly across subjects, indicating high within-visit repeatability in healthy subjects.</p>