We characterized the short-interval intracortical facilitation (SICF) via modulation of transcranial magnetic stimulation (TMS) induced motor evoked potentials (MEPs) using paired-pulse stimulation, and analyzed the interactions with known SICF I-wave behavior. The objective was to optimize individual SICF to enhance TMS effects in motor mapping and therapeutic stimulations. We applied navigated TMS in nine healthy volunteers to study SICF. MEPs were measured for baseline using single-pulse TMS, and subsequently, paired-pulse TMS was applied to study SICF. The interstimulus interval (ISI) between the pulses was varied between 1.2 and 4.3 ms at 0.1 ms intervals. Ten MEPs were measured from three muscles (FDI, APB and ADM) in the dominant hand of the volunteer. We then fitted a 3-peak Gaussian model to the individual paired-pulse MEP vs. ISI curves to characterize each peak by latency, amplitude and width. Individual SICF I-wave interaction characteristics were successfully determined. The average peak latencies were 1.36 (I1-wave), 2.80 (I2-wave) and 4.29 (I3-wave) for the targeted FDI muscle. The peak amplitudes differed depending on the muscle (p = 0.001), with ADM muscle exhibiting greatest SICF effect, but no significant difference between the three peaks. In addition, the peak widths differed between all muscles (p<0.001), second peak being the widest. In conclusion, the individual SICF I-wave interaction characteristics were successfully determined revealing significant differences in peak features. This could enable application of SICF for enhancement of TMS effects in therapy, cortical mapping and basic neuroscience applications.